DGH - Dissertações de mestrado
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- Hazard characterisation of bisphenol A alternatives to improve risk assessment for human health: genotoxic and carcinogenic effects in mammalian cellsPublication . Pereira, Maria João Rodrigues; Silva, Maria João; Farinha, CarlosBisphenol A (BPA) is a compound used in the production of epoxy resins, polycarbonate plastics and as an additive (e.g. in thermal paper). It is present in several different products and has been detected both in the environment and in human matrices. BPA is a known endocrine disruptor, with several studies linking it to multiple harmful health effects. Therefore, there is an effort to phase out its use, but also to replace it with alternative substances. Various alternatives are already being used and have been detected in the environment and human matrices. Furthermore, some harmful health effects have also been reported for those substances (albeit not as many as BPA), justifying the need for more research on these alternatives. This thesis is part of the Partnership for the Assessment of Risks from Chemicals (PARC), that prioritized alternatives based on the lack of data on their effects on human health and due to human exposure to them occurring or being likely to occur. This thesis focused on BPS-MAE and BPAP, aiming to contribute to their hazard assessment, through the characterisation of their in vitro genotoxic and carcinogenic potential. The former was assessed for BPS-MAE and BPAP with the Cytokinesis-Block Micronucleus assay, in human peripheral blood lymphocytes. The results suggest that BPS-MAE and BPAP do not have a genotoxic effect at the concentrations and exposure times tested. Genotoxic and non-genotoxic carcinogenicity of BPAP and BPA was ascertained with the Cell Transformation assay, in Bhas 42 cells. BPA was tested to allow inter-laboratory comparison of results and assay optimisation. The results indicate that neither BPAP nor BPA have potential carcinogenic activity at the concentrations and treatment durations tested. The data obtained will help eliminating existing data gaps, aid to improve these alternatives’ risk assessment and contribute to the formulation of legislation, if necessary.
- Statistical analysis of longitudinal RBC omics dataPublication . Silva, Carolina; Antunes, Marília; Penque, DeborahRed blood cells (RBCs) are emerging as important modulators of the immune system. Despite evidence that alterations in RBC functionality are associated with disease severity in COVID-19 patients, there is no information regarding the impact of RBC activity on the immune response to COVID-19 vaccination. This work aims to establish an adequate methodology for the statistical analysis of longitudinal RBC metabolomics data collected during COVID-19 vaccination (n=22, 5 time points) to identify metabolites with significant changes throughout the immunization process. For the pre-treatment of the metabolomics data set, different pre-treatment methodologies comprised of imputation and normalization steps were compared to investigate which algorithm and application order was more adequate. Testing of these methods showed that normalization followed by kNN imputation using cosine distance was highlighted as the best-performing pre-treatment strategy. Following its application, generalized estimating equations (GEEs) created from the normalized data led to the identification of 30 metabolites with significant changes in concentration between different time points of COVID-19 vaccination. Significant RBC metabolites were linked to major metabolic pathways in the cells, such as the metabolism of amino acids and purines, and the transport of small molecules through the cellular membrane. Some of these metabolites were discovered to have relevant functions in the development of an effective immune response against infections, like COVID-19. The connections between these metabolites and the defense mechanisms commonly used by cells to fight viral infections offer a strong clue for the immune functions that those metabolites may have in the human body, suggesting that the RBC metabolism could play a significant part in the generation of an immune response to COVID-19 vaccination. Further work is in progress to integrate and correlate proteomic data retrieved from the same longitudinal experiment for a comprehensive depiction of the RBC function in the COVID-19 vaccine-induced immunization process.
- 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.
- Repurposing of CFTR modulator drugs in the context of colorectal cancerPublication . Vincente, Luana Pimenta; Matos, Paulo; Jordan, PeterColorectal cancer (CRC) remains one of the leading causes of cancer death worldwide and is considered to arise from genetic and epigenetic changes due to interactions between the tumor and the microenvironment that surrounds it. Recently, the chloride and bicarbonate channel CFTR (cystic fibrosis transmembrane conductance regulator) was implicated in CRC etiology, since a decreased CFTR expression is associated to higher aggressiveness and lower survival in sporadic CRC. Moreover, CFTR mutations are the cause for the autosomal recessive disease cystic fibrosis (CF), and individuals with CF have a higher risk of developing CRC. Several CFTR modulator drugs have been recently clinically approved to improve CFTR functional expression in CF individuals. The current Masters’ project aimed to determine if these drugs can also be used to improve CFTR abundance in non-CF CRC cells, and whether these could be used to reduce their oncogenic properties. For this purpose, four CRC cell lines, with different CFTR expression levels, were cultured and treated with three CFTR modulator drugs, individually and in combination. It was observed that the combination treatment with the three drugs significantly increased CFTR protein levels in the Caco-2 and DLD-1 cells, but had no significant impact in either HCT116 or HT29 cells, likely due to their particular genetic and epigenetic backgrounds. Importantly, treatment with CFTR modulators significantly inhibited migration of Caco-2 and DLD-1 cells, without markedly impacting their viability. These findings suggest that CFTR modulators have potential as therapeutic agents to counteract the oncogenic properties of CRC cells with specific genetic and epigenetic profiles. However, the impact of CFTR modulator treatment in CRC development will need to be validated in vivo using mouse models. Repurposing these modulators for CRC treatment could enhance outcomes for CRC patients while also reducing costs for CF patients by expanding the clinical applications of these drugs.
- Impact of BCL-6 downregulation in the oncogenic properties of breast cancer cellsPublication . Jorge, João Miguel Dyson de Lima; Barros, Patrícia; Jordan, PeterBreast cancer (BC) incidence has risen over the past two decades, now being the second most prevalent cancer worldwide and the fourth leading cause of cancer-related deaths. Despite advancements in BC treatment, challenges like acquired resistance, recurrence, and metastasis persist. BCL-6, a transcriptional repressor, plays a controversial role in BC development. It is overexpressed in approximately half of primary tumors across all subtypes, correlating with poorer patient prognosis. Conversely, its downregulation is linked to disease progression and metastasis, highlighting the critical need for a deeper understanding of BCL-6's dual role in BC pathogenesis. This study used RNA interference to explore the impact of BCL-6 depletion on the oncogenic progression of MCF-7 cells, a low-tumorigenic estrogen receptor-alpha-positive (ERα+) cell line. While BCL-6 is known to regulate mammary cell proliferation and differentiation, its depletion did not affect MCF-7 cell proliferation or viability but significantly reduced their individual and collective migratory properties. An RNA microarray analysis identified a set of genes upregulated following BCL-6 depletion, including S100A7, previously reported to inhibit MCF-7 cell migration and invasion in ERα+ BC cells. However, our findings showed that S100A7 downregulation alone did not affect MCF-7 migration. Moreover, simultaneous depletion of BCL-6 and S100A7 failed to restore MCF-7 cell migratory behavior. Our results suggest that increased expression of BCL-6 is linked to increased cell migration but is independent of S100A7 upregulation. Further studies are required to clarify the role of BCL-6 in BC, including disease progression.
- Assessment of genotoxicity biomarkers in the scope of a human biomonitoring study in workers from E-waste management industriesPublication . Lopes Rosário, Rita Isabel; Silva, Maria João; Pina Martins, FranciscoElectrical and electronic waste (e-waste) represents a pressing global challenge with its rapid growth and hazardous composition. This recycling sector often involves inadequate worker safety, exposing e-workers to harmful substances like heavy metals and flame retardants via several routes, causing significant short- and long-term health risks. Human Biomonitoring (HBM) is a useful tool in assessing exposure and associated health outcomes through biomarkers like micronucleus (MN) in blood or epithelial cells, enabling the identification of early biological changes and linking exposure to disease. This HBM study used two assays,- the Buccal Micronucleus Cytome (BMNCyt) assay and the Cytokinesis-Block Micronucleus Cytome (CBMNCyt) assay,- to assess potential genotoxic effects from occupational e-waste exposure. The BMNCyt assay, conducted under the HBM4EU initiative, targets buccal mucosa epithelial cells, a primary barrier against hazardous agents, thus assessing local genotoxic effects. The CBMNCyt assay in peripheral blood lymphocytes, conducted under the PARC Project, reliably measures structural and numerical chromosomal changes, reflecting a systemic effect. This research aimed to assess early biological effects from exposure to pollutants from e-waste in in PBL and buccal epithelial cells of European e-waste workers, comparatively with control groups. The BMNCyt assay showed no significant differences in MN frequency between the exposed and control groups, while the CBMNCyt assay detected significantly increased frequencies of MN in exposed compared with non-exposed groups. Factors like small sample sizes, interindividual differences, and the use of protective equipment might have influenced results. Demographic/lifestyle variables showed differing impacts on MN formation between assays, but also potential influence, thus the importance of their consideration. Concluding, expanding e-waste occupational health research to include more workers/activities within the waste management industry and broader biomonitoring efforts is paramount. Boosting the understanding of health risks associated with those activities will help developing protective measures and mitigation strategies to safeguard the exposed workers’ health.
- 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.
- The mechanism of nonsense-mediated mRNA decay and its playersPublication . Subtil, Catarina; Loison, Luísa; Santos, Rafaela LacerdaNonsense-mediated mRNA decay (NMD) is a post-transcriptional surveillance mechanism harbouring two functions: identification and degradation of transcripts containing premature translation-termination codons (PTC), preventing deleterious effects in the cell; and downregulation of mRNAs in response to cellular needs, maintaining the quality of gene expression. One-third of gene mutations in human genetic diseases, including cancer, are due to nonsense mutations or frameshift that result in transcripts harbouring nonsense codons and can be eliminated by NMD. The several factors involved in this mechanism may act in diverse ways depending on the set of transcripts to be regulated, contributing to the branching of this pathway. Cytoplasmic DIS3 exosome independent 3′-5′ exoribonuclease 2 (DIS3L2) has been reported as one of the factors to induce NMD targets decay. Therefore, this study aims to enlighten how DIS3L2 functions in NMD: i) analyse the correlation between the distinct branches of NMD and cervical and uterus cancer; ii) investigate which branch guides DIS3L2-mediated degradation; and iii) test which region of the NMD/DIS3L2-targets mediate DIS3L2 degradation through a system of hybrid-genes. For our first aim, we detected no correlation between any of the branches of NMD and uterus and cervical cancer. Each factor acts independently. In our second objective, we analysed the mRNA expression of five transcripts, but none displayed a significant alteration in their expression to infer a correlation between DIS3L2 and a particular NMD branch. Relatively to the last aim, we successfully cloned three out of the four constructs but due to time constrictions we could not continue. Nonetheless, further testing is needed to better understand this mechanism and how transcript degradation is mediated, including the diverse factors needed for its activation, which might be the key to future advanced therapeutic strategies.
- Regulation of the alternative splicing of RAC1B in tumor cellsPublication . Bizarro, Inês; Gonçalves, Vânia; Jordan, PeterCancer is a molecularly heterogeneous disease that presents genetic modifications in different alternative pathways. Namely, a subgroup of colorectal cancer (CRC) is characterized by the simultaneous presence of an oncogenic mutation in BRAF and overexpression of RAC1B, an alternative splicing variant of the small GTPase RAC1. Together, these two changes stimulate signalling pathways that induce the proliferation and survival of CRC cells. Previously, the splicing factors (SFs) ESRP1 and SRSF1 were reported to promote RAC1B overexpression in this type of tumor, while SRSF3 inhibited it. However, the overexpression of RAC1B has also been identified in breast and lung tumors. As such, this work aimed to study the modulatory role of ESRP1, SRSF1 and SRSF3 on RAC1B alternative splicing in breast and lung cancer cells, using CRC cells as an experimental control since the role of these SFs has already been documented in these types of tumor. The SFs were overexpressed in the cells by co-transfection with a RAC1 minigene and the expression levels of the minigene-derived transcripts were analysed by RT-PCR. Next, the SFs endogenous expression was depleted by siRNA transfection and the endogenous levels of RAC1B transcript and protein were assessed through RT-PCR and Western blot, respectively. The obtained results indicate a role for SRSF1 and SRSF3 in positively and negatively modulating RAC1B alternative splicing, respectively, in both breast and lung cancer cells, as previously described for CRC. Intriguingly, ESRP1 inhibited RAC1B alternative splicing in these cells, revealing an opposite role to what was previously observed for CRC. Although future studies should be performed to confirm these results, ESRP1 and SRSF3 act as inhibitors of RAC1B alternative splicing whereas SRSF1 acts as an enhancer, in both breast and lung cancer cells.
- A tradução não-canónica da proteína UPF1 (up-frameshift 1) e a sua relevância na tumorigénese do cancro colorretalPublication . Antunes Elias, Adriana; Santos, Rafaela; Romão, LuísaA iniciação da tradução é o passo limitante da síntese proteica. Em condições de stresse, a tradução canónica é inibida e a tradução de transcritos específicos é mantida por mecanismos alternativos, como os que envolvem IRES (internal ribosome entry site). A UPF1 (up-frameshift 1) contribui para a tumorigénese no cancro colorretal (CRC, colorectal cancer). Anteriormente neste laboratório verificouse que a região 5'UTR (5’untranslated region) do transcrito de UPF1 apresenta atividade IRES e que esta é mantida em condições de stresse. Assim, esta tese teve como objetivo aferir como a tradução da UPF1 mediada por IRES pode contribuir para a progressão do CRC. As análises in silico realizadas através da plataforma Xena, para medir a variação dos níveis de expressão do transcrito e da proteína entre diferentes tipos de cancro e entre tecidos normais e cancerígenos do cólon, mostraram que a expressão de mRNA e proteína é superior nos tecidos de CRC do que noutros tipos de cancro e também em comparação com os tecidos normais do cólon, sugerindo que a expressão da UPF1 é superior quando esta contribui para a tumorigénese. Adicionalmente, a análise da expressão endógena da UPF1 em células epiteliais cultivadas da mucosa normal do cólon humano (NCM460) e em linhas celulares correspondentes a diferentes estádios de desenvolvimento de CRC (HT29, HCT116 e SW480), expostas a 1 μM de tapsigargina (que induz o stresse do retículo endoplasmático e, portanto, inibe a tradução canónica), revelou que a expressão da UPF1 é mantida em condições nas quais a tradução canónica é inibida, sugerindo que ocorre tradução mediada por IRES e que esta permite a manutenção dos níveis de UPF1 nessas condições. Concluindo, a tradução mediada por IRES contribui para a síntese da UPF1 em tecidos de CRC, o que, por sua vez, contribui para a progressão deste tipo de cancro.