Browsing by Author "Faustino, Paula"
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- Alpha-thalassemia due to novel deletions and complex rearrangements in the subtelomeric region of chromosome 16pPublication . Ferrão, José; Silva, Marisa; Gonçalves, Lúcia; Gomes, Susana; Loureiro, Pedro; Coelho, Andreia; Miranda, Armandina; Seuanes, Filomena; Batalha Reis, Ana; Pina, Francisca; Maia, Raquel; Kjollerstrom, Paula; Monteiro, Estela; F. Lacerda, João; Lavinha, João; Gonçalves, João; Faustino, PaulaIntroduction: Inherited deletions removing the α-globin genes and/or their upstream regulatory elements (MCSs) give rise to alpha-thalassemia, one of the most common genetic recessive disorders worldwide. The pathology is characterized by microcytic hypochromic anemia due to reduction of the α-globin chain synthesis, which are essential for hemoglobin tetramerization. Material and Methods: In order to clarify the suggestive α-thalassemia phenotype in eleven patients, we performed Multiplex Ligation-dependent Probe Amplification with commercial and synthetic engineered probes, gap-PCR, and Sanger sequencing to search for deletions in the subtelomeric region of chromosome 16p. Results: We have identified five distinct large deletions, two of them novel, and one indel. The deletions range from approximately 3.3 to 323 kb, and i) remove the whole α-globin cluster; or ii) remove exclusively the upstream regulatory elements leaving the α-globin genes structurally intact. The indel consists in the loss of MCS-R2 (HS-40), which is the most important distal regulatory element for the α-globin gene expression, and the insertion of 39 bp, seemingly resulting from a complex rearrangement involving two DNA segments (probably from chromosome 3q) bridging the deletion breakpoints with a CC-bp orphan sequence in between. Finally, in one patient no α-globin deletion or point mutation were found. This patient revealed to be a very unusual case of acquired alpha-thalassemia associated with a myelodysplastic syndrome. Conclusions: Our study widens the spectrum of molecular lesions by which α-thalassemia may occur and emphasizes the importance of diagnosing large α-zero-deletions to provide patients with appropriate genetic counseling.
- Alpha-thalassemia due to novel deletions and complex rearrangements in the subtelomeric region of chromosome 16pPublication . Ferrão, José; Silva, Marisa; Gonçalves, Lúcia; Gomes, Susana; Loureiro, Pedro; Coelho, Andreia; Miranda, Armandina; Seuanes, Filomena; Batalha Reis, Ana; Valtonen-André, Camila; Sonesson, Annika; Pina, Francisca; Maia, Raquel; Kjollerstrom, Paula; Monteiro, Estela; F. Lacerda, João; Lavinha, João; Gonçalves, João; Faustino, PaulaIntroduction: Inherited deletions removing the α-globin genes and/or their upstream regulatory elements (MCSs) give rise to alpha-thalassemia, one of the most common genetic recessive disorders worldwide. The pathology is characterized by microcytic hypochromic anemia due to reduction of the α-globin chain synthesis, which are essential for hemoglobin tetramerization. Material and Methods: In order to clarify the suggestive α-thalassemia phenotype in eleven patients, we performed Multiplex Ligation-dependent Probe Amplification with commercial and synthetic probes, gap-PCR, and Sanger sequencing to search for deletions in the subtelomeric region of chromosome 16p. Results: We have identified six distinct large deletions, three of them novel, and one indel. The deletions range from approximately 3.3 to 323 kb, and i) remove the whole α-globin cluster; or ii) remove exclusively the upstream regulatory elements leaving the α-globin genes structurally intact. The indel consists in the loss of MCS-R2 (HS-40), which is the most important distal regulatory element for the α-globin gene expression, and the insertion of 39 nt, seemingly resulting from a complex rearrangement involving two DNA segments (probably from chromosome 3q), bridging the deletion breakpoints with a CC-bp orphan sequence in between. Finally, in one patient no α-globin deletion or point mutation were found. This patient revealed to have acquired alpha-thalassemia associated with a myelodysplastic syndrome. Conclusions: Our study widens the spectrum of molecular lesions by which α-thalassemia may occur and emphasizes the importance of diagnosing large α0-deletions to provide patients with appropriate genetic counseling.
- Alterações fenotípicas e genéticas do metabolismo do ferro numa população portuguesa com doença de Alzheimer: potenciais implicações no conhecimento da fisiopatologia e no diagnóstico desta demênciaPublication . Crespo, A.C.; Silva, B.; Marques, L.; Marcelino, E.; Maruta, C.; Costa, S.; Timóteo, A.; Vilares, A.; Couto, F.S.; Faustino, Paula; Correia, A.P.; Verdelho, A.; Porto, G.; Guerreiro, M.; Herrero, A.; Costa, C.; Mendonça, A.; Martins, M.; Costa, L.
- Alternative polyadenylation and nonsense-mediated decay coordinately regulate the human HFE mRNA levelsPublication . Martins, Rute; Proença, Daniela; Silva, Bruno; Barbosa, Cristina; Silva, Ana Luísa; Faustino, Paula; Romão, LuísaNonsense-mediated decay (NMD) is an mRNA surveillance pathway that selectively recognizes and degrades defective mRNAs carrying premature translation-termination codons. However, several studies have shown that NMD also targets physiological transcripts that encode full-length proteins, modulating their expression. Indeed, some features of physiological mRNAs can render them NMD-sensitive. Human HFE is a MHC class I protein mainly expressed in the liver that, when mutated, can cause hereditary hemochromatosis, a common genetic disorder of iron metabolism. The HFE gene structure comprises seven exons; although the sixth exon is 1056 base pairs (bp) long, only the first 41 bp encode for amino acids. Thus, the remaining downstream 1015 bp sequence corresponds to the HFE 39 untranslated region (UTR), along with exon seven. Therefore, this 39 UTR encompasses an exon/exon junction, a feature that can make the corresponding physiological transcript NMD-sensitive. Here, we demonstrate that in UPF1-depleted or in cycloheximide-treated HeLa and HepG2 cells the HFE transcripts are clearly upregulated, meaning that the physiological HFE mRNA is in fact an NMD-target. This role of NMD in controlling the HFE expression levels was further confirmed in HeLa cells transiently expressing the HFE human gene. Besides, we show, by 39-RACE analysis in several human tissues that HFE mRNA expression results from alternative cleavage and polyadenylation at four different sites – two were previously described and two are novel polyadenylation sites: one located at exon six, which confers NMD-resistance to the corresponding transcripts, and another located at exon seven. In addition, we show that the amount of HFE mRNA isoforms resulting from cleavage and polyadenylation at exon seven, although present in both cell lines, is higher in HepG2 cells. These results reveal that NMD and alternative polyadenylation may act coordinately to control HFE mRNA levels, possibly varying its protein expression according to the physiological cellular requirements.
- An overview of molecular basis of iron metabolism regulation and the associated pathologiesPublication . Silva, Bruno; Faustino, PaulaIron is essential for several vital biological processes. Its deficiency or overload drive to the development of several pathologies. To maintain iron homeostasis, the organism controls the dietary iron absorption by enterocytes, its recycling by macrophages and storage in hepatocytes. These processes are mainly controlled by hepcidin, a liver-derived hormone which synthesis is regulated by iron levels, inflammation, infection, anemia and erythropoiesis. Besides the systemic regulation of iron metabolism mediated by hepcidin, cellular regulatory processes also occur. Cells are able to regulate themselves the expression of the iron metabolism-related genes through different post-transcriptional mechanisms, as the alternative splicing, microRNAs, the IRP/IREs system and the proteolytic cleavage. Whenever those mechanisms are disturbed, due to genetic or environmental factors, iron homeostasis is disrupted and iron related pathologies may arise.
- Análise Genómica - Dos métodos tradicionais às novas metodologiasPublication . Faustino, PaulaNeste módulo será apresentada a evolução dos métodos de determinação da ordem precisa de nucleótidos nas moléculas de DNA/RNA. Iniciar-se-á pela sequenciação de Sanger que veio permitir o conhecimento da sequência completa de genes e de genomas. Seguir-se-á a apresentação da evolução da automatização da sequenciação em escala de altíssima eficiência (high-throughput), a chamada sequenciação de nova geração, e a sua aplicação em diversas áreas da genómica, como por exemplo, na identificação de novas mutações/genes envolvidos em doenças genéticas sem diagnóstico conhecido, e no conhecimento da variabilidade de genomas individuais em diversos organismos incluindo humanos (genómica individual), abrindo portas para novas áreas da biomedicina, como a medicina personalizada e a farmacogenómica.
- Analysis of Genes Involved in Oxidative Stress and Iron Metabolism in Heart Failure: A Step Forward in Risk StratificationPublication . Silva, Pedro X.; Aguiar, Laura; Gaspar, Marcos; Faustino, Paula; Falcão, Luiz M.; Barbosa, Mário; Bicho, Manuel; Inácio, ÂngelaIntroduction: Heart failure (HF) is a clinical syndrome characterized by cardinal symptoms that may be accompanied by signs. It results from structural and/or functional abnormalities of the heart leading to elevated intracardiac pressures and/or inadequate cardiac output at rest and/or during exercise. The prevalence of iron deficiency and anemia justifies the current guidelines recommendation of screening. Genes HP, ACE, MTHFR, HFE, and CYBA are involved in oxidative mechanisms, iron metabolism, and hematologic homeostasis. This study investigates the contribution of variants Hp1/2 (HP), I/D (ACE), C677T (MTHFR), C282Y and H63D ( HFE), and C242T (CYBA) to the development of HF, either independently or in epistasis. Methods: We used a database of 389 individuals, 143 HF patients, and 246 healthy controls. Genotypes were characterized through PAGE electrophoresis, PCR, PCR-RFLP, and multiplex-ARMS. Data analysis was performed with the SPSS® 26.0 software (IBM Corp., Armonk, NY). Results: We observed a significant association between the MTHFR gene and HF predisposition. The presence of allele T and genotype CT constituted risk, while genotype CC granted protection. Epistatic interactions revealed risk between genotype II of the ACE gene and genotypes CC (C282Y) or HH (H63D) of the HFE gene. Risk was also observed for interactions between genotype CC (CYBA) and genotypes 2-2 (HP), CT (MTHFR), or HH (HFE-H63D). Conclusion: We concluded that genes HP, ACE, MTHFR, HFE, and CYBA contribute to the susceptibility for HF, individually or in epistasis. This study contributes to the clarification of the role that genes involved in oxidative mechanisms and iron metabolism play in the physiopathology of HF. It is, therefore, a step forward in risk stratification and personalized medicine.
- Analysis of malaria associated genetic traits in Cabo Verde, a melting pot of European and sub Saharan settlersPublication . Alves, Joana; Machado, Patrícia; Silva, João; Gonçalves, Nilza; Ribeiro, Letícia; Faustino, Paula; Rosário, Virgílio Estólio do; Manco, Licínio; Gusmão, Leonor; Amorim, António; Arez, Ana PaulaMalaria has occurred in the Cabo Verde archipelago with epidemic characteristics since its colonization. Nowadays, it occurs in Santiago Island alone and though prophylaxis is not recommended by the World Health Organization, studies have highlight the prospect of malaria becoming a serious public health problem as a result of the presence of antimalarial drug resistance associated with mutations in the parasite populations and underscore the need for tighter surveillance. Despite the presumptive weak immune status of the population, severe symptoms of malaria are not observed and many people present a subclinical course of the disease. No data on the prevalence of sicklecell trait and red cell glucose-6-phosphate dehydrogenase deficiency (two classical genetic factors associated with resistance to severe malaria) were available for the Cabo Verde archipelago and, therefore, we studied the low morbidity from malaria in relation to the particular genetic characteristics of the human host population. We also included the analysis of the pyruvate kinase deficiency associated gene, reported as putatively associated with resistance to the disease. Allelic frequencies of the polymorphisms examined are closer to European than to African populations and no malaria selection signatures were found. No association was found between the analyzed human factors and infection but one result is of high interest: a linkage disequilibrium test revealed an association of distant loci in the PKLR gene and adjacent regions, only in non-infected individuals. This could mean a more conserved gene region selected in association to protection against the infection and/or the disease.
- Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7 kb α-thalassemia deletionPublication . Pena, Rita; Lopes, Pedro; Gaspar, Gisela; Miranda, Armandina; Faustino, PaulaBackground: The α-Major Regulatory Element (α-MRE), also known as HS-40, is located upstream of the α-globin gene cluster and has a crucial role in the long-range regulation of the α-globin gene expression. This enhancer is polymorphic and several haplotypes were identified in different populations, with haplotype D almost exclusively found in African populations. The purpose of this research was to identify the HS-40 haplotype associated with the 3.7 kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and determine its ancestry and influence on patients' hematological phenotype. Methods and results: We selected 111 Portuguese individuals previously analyzed by Gap-PCR to detect the presence of the -α3.7del: 50 without the -α3.7del, 34 heterozygous and 27 homozygous for the -α3.7del. The HS-40 region was amplified by PCR followed by Sanger sequencing. Four HS-40 haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between individuals with and without the -α3.7del, being haplotype D and genotype AD the most prevalent in patients with this deletion in homozygosity. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are separated from these and found more closely related to the African population. Conclusion: This study revealed for the first time an association of the HS-40 haplotype D with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have clinical importance as in vitro analysis of haplotype D showed a decrease in its enhancer activity on α-globin gene.
- Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7kb α-thalassemia deletionPublication . Pena, Rita; Lopes, Pedro; Gaspar, Gisela; Miranda, Armandina; Faustino, PaulaThe α-major regulatory element (known as HS-40) has a crucial role in the long-range regulation of the α-globin gene expression. This element is genetically polymorphic and six haplotypes (A to F) have been identified in different populations, with haplotype D almost exclusively found in African populations. This study aimed to identify the HS-40 haplotype associated with the common 3.7kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and investigate its ancestry. We searched for the -α3.7del in 111 selected Portuguese individuals by Gap-PCR. In addition, a DNA fragment containing the HS-40 was amplified by PCR and Sanger sequenced. Statistical analysis was performed using R software. Fifty individuals have the wild-type α-globin genotype (group I), 34 are heterozygous for the -α3.7del (group II) and 27 are homozygous (group III). Regarding the HS-40, four haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between groups with and without the -α3.7del (p<0.001), being haplotype D and genotype AD the most prevalent in group III. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are split from these and found more related to the African population. This study revealed for the first time an association of a specific HS-40 haplotype with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have a clinical importance as in vitro analysis of haplotype D showed a descrease in its enhancer activity on α-globin genes.