Browsing by Author "Vieira, Luis"
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- Annual Scientific Report of the Center for Toxicogenomics and Human HealthPublication . Penque, Deborah; Vieira, Luis; Gonçalves, João; Louro, Henriqueta; Silva, Maria João
- Characterization of the Human Papillomavirus 16 Oncogenes in K14HPV16 Mice: Sublineage A1 Drives Multi-Organ CarcinogenesisPublication . Cochicho, Daniela; Nunes, Alexandra; Gomes, João Paulo; Martins, Luís; Cunha, Mário; Medeiros-Fonseca, Beatriz; Oliveira, Paula; Bastos, Margarida M.S.M.; Medeiros, Rui; Mendonça, Joana; Vieira, Luis; Gil da Costa, Rui M.; Felix, AnaThe study of ()-induced carcinogenesis uses multiple in vivo mouse models, one of which relies on the cytokeratin 14 gene promoter to drive the expression of all HPV early oncogenes. This study aimed to determine the HPV16 variant and sublineage present in the K14HPV16 mouse model. This information can be considered of great importance to further enhance this K14HPV16 model as an essential research tool and optimize its use for basic and translational studies. Our study evaluated HPV DNA from 17 samples isolated from 4 animals, both wild-type (n = 2) and HPV16-transgenic mice (n = 2). Total DNA was extracted from tissues and the detection of HPV16 was performed using a qPCR multiplex. HPV16-positive samples were subsequently whole-genome sequenced by next-generation sequencing techniques. The phylogenetic positioning clearly shows K14HPV16 samples clustering together in the sub-lineage A1 (NC001526.4). A comparative genome analysis of K14HPV16 samples revealed three mutations to the human papillomaviruses type 16 sublineage A1 representative strain. Knowledge of the HPV 16 variant is fundamental, and these findings will allow the rational use of this animal model to explore the role of the A1 sublineage in HPV-driven cancer.
- Defeitos Genéticos das Doenças Mitocondriais: Abordagem por Sequenciação de Nova GeraçãoPublication . Nogueira, Célia; Pereira, Cristina; Silva, Lisbeth; Vieira, Luis; Leão Teles, Elisa; Rodrigues, Esmeralda; Campos, Teresa; Janeiro, Patricia; Costa, Claúdia; Gaspar, Ana; Soares, Gabriela; Bandeira, Anabela; Martins, Esmeralda; Santos, Helena; Vilarinho, LauraObjetivos:O objetivo deste projeto de investigação é desenvolver uma estratégia de sequenciação de nova geração para a identificação das alterações genéticas em doentes suspeitos de doenças mitocondriais sem caracterização molecular.
- Diagnóstico das Doenças Mitocondriais por Sequenciação de Nova GeraçãoPublication . Nogueira, Célia; Pereira, Cristina; Silva, Lisbeth; Rodrigues, Esmeralda; Janeiro, Patricia; Sequeira, Sílvia; Santos, Helena; Martins, Esmeralda; Vilarinho, Laura; Vieira, Luis; Leão Teles, Elisa; Campos, Teresa; Costa, Cláudia; Gaspar, Ana; Dupont, Juliette; Soares, Gabriela; Bandeira, Anabela; Magalhães, Marina; Vieira, José PedroIntrodução e objetivos: As doenças mitocondriais constituem um importante grupo de doenças metabólicas de expressão clínica heterogénea, para as quais não existe uma terapia eficaz. Estas patologias podem ser causadas por defeitos genéticos quer no genoma mitocondrial, quer no nuclear. A sequenciação de nova geração (NGS) revolucionou o diagnóstico molecular destas doenças, uma vez que tem capacidade de gerar uma enorme quantidade de dados num curto espaço de tempo a um custo acessível. O objetivo deste estudo [Financiado pela FCT (PTDC/DTP-PIC/2220/2014) e pelo Norte 2020 (NORTE-01-0246-FEDER-000014)] é desenvolver uma estratégia de NGS para permitir o diagnóstico genético de doentes suspeitos de doenças mitocondriais.
- Distribution and Clinical Significance of HPV16 Variants in Head and Neck Squamous Cell Carcinomas: Data from a Portuguese Cohort and Systematic ReviewPublication . Cochicho, Daniela; Nunes, Alexandra; Sobral, Daniel; Gomes, João P.; Esteves, Susana; Mendonça, Joana; Vieira, Luis; Martins, Luís; Cunha, Mario; Montalvão, Pedro; Magalhães, Miguel; Gil da Costa, Rui M.; Félix, AnaIntroduction: Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aimed to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical pathological characteristics and patient survival. Methods: We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing was used to obtain whole-genome sequences, and variants were established based on phylogenetic classification. Results: 74% of samples clustered in lineage A, 5.7% in lineage B, 2.9% in lineage C, and 17.1% in lineage D. Comparative genome analysis revealed 243 single nucleotide variations. Of these, one hundred were previously reported, according to our systematic review. No significant associations with clinical pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V, and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. Conclusion: These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.
- Next Generation Sequencing Improves Mitochondrial Diseases DiagnosisPublication . Nogueira, Célia; Vilarinho, Laura; Pereira, Cristina; Silva, Lisbeth; Vieira, Luis; Leão Teles, Elisa; Rodrigues, Esmeralda; Campos, Teresa; Janeiro, Patrícia; Costa, Claúdia; Gaspar, Ana; Soares, Gabriela; Bandeira, Anabela; Martins, Esmeralda; Magalhães, Marina; Sequeira, Sílvia; Vieira, José Pedro; Santos, HelenaObjectives: The overall aim of our research project was to develop a Next Generation Sequencing strategy to identify nuclear disease causing-mutations in patients suspicious of mitochondrial disorders but without molecular etiology.
- Next generation sequencing: a golden tool in mitochondrial diseasesPublication . Nogueira, Celia; Pereira, Cristina; Silva, Lisbeth; Vieira, Luis; Leão Teles, Elisa; Campos, Teresa; Rodrigues, Esmeralda; Martins, Esmeralda; Bandeira, Anabela; Soares, Gabriela; Janeiro, Patricia; Costa, Claudia; Gaspar, Ana; Santos, Helena; Vilarinho, LauraThe development of Next Generation Sequencing (NGS) has revolutionized the diagnostic approach of mitochondrial disorders, particularly in children. The purpose of our project is to develop a NGS strategy to identify the genetic defect in 250 patients, to confirm the clinical diagnosis of the disease.
- Next-generation sequencing of iron-metabolism related genes in Portuguese patients with iron overload: novel pathogenic genetic variantsPublication . Faria, Ricardo; Silva, Bruno; Silva, Catarina; Vieira, Luis; Loureiro, Pedro; Gomes, Susana; Gonçalves, João; Rivera, Isabel; Fraga, Sofia; Fleming, Rita; Faustino, PaulaObjective: In Southern European countries up to one-third of the patients with hereditary hemochromatosis (HH) do not present the common HFE risk genotype. In order to investigate the molecular basis of these cases we have designed a gene panel for rapid and simultaneous analysis of 6 HH-related genes (HFE, TFR2, HJV, HAMP, SLC40A1 and FTL) by next-generation sequencing (NGS). Materials and Methods: Eighty-eight iron overload Portuguese patients, negative for the common HFE mutations, were analysed. A TruSeq Custom Amplicon kit (TSCA, by Illumina) was designed in order to generate 97 amplicons covering exons, intron/exon junctions and UTRs of the mentioned genes with a cumulative target sequence of 12115bp. Amplicons were sequenced in the MiSeq instrument (IIlumina) using 250bp paired-end reads. Sequences were aligned against human genome reference hg19 using alignment and variant caller algorithms in the MiSeq reporter software. Novel variants were validated by Sanger sequencing and their pathogenic significance were assessed by in silico studies. Results: We found a total of 55 different genetic variants. These include novel pathogenic missense and splicing variants (in HFE and TFR2), a very rare variant in IRE of FTL, a variant that originates a novel translation initiation codon in the HAMP gene, among others. Conclusion: The merging of TSCA methodology and NGS technology appears to be an appropriate tool for simultaneous and fast analysis of HH-related genes in a large number of samples. However, establishing the clinical relevance of NGS-detected variants for HH development remains a hard-working task, requiring further functional studies.
- Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondiiPublication . Vilares, Anabela; Borges, Vítor; Sampaio, Daniel; Ferreira, Idalina; Martins, Susana; Vieira, Luis; Gargaté, Maria João; Gomes, João PauloAdvances in molecular epidemiology of Toxoplasma gondii are hampered by technical and cost-associated hurdles underlying the acquisition of genomic data from parasites. In order to implement an enhanced genotyping approach for molecular surveillance of T. gondii, we applied a multi-locus amplicon-based sequencing strategy to samples associated with human infection. This approach, targeting genome-dispersed polymorphic loci potentially involved in adaptation and virulence, genetically discriminated almost all 68 studied strains and revealed a scenario of marked genomic mosaicism. Two-thirds (n = 43) of all strains were classified as recombinant, although recombination seemed to be linked to the classical archetypal lineage. While 92% of the Sag2 archetype I strains revealed genetic mosaicism, only 45% of Sag2 archetype II strains were identified as recombinant. Contrarily to the virulence-associated archetype I, most type II strains (regardless of their recombination background) were non-virulent in mouse. Besides Sag2, some of the newly studied loci (namely the type I/I-like alleles of Sag1, B17, PK1, and Sag3 and type III/III-like alleles of TgM-A) constitute promising candidates to rapidly infer T. gondii mouse virulence. Our successful attempt to capture microsatellite length variation launches good perspectives for the straightforward transition from the laborious intensive historical method to more informative next-generation sequencing (NGS)/bioinformatics-based methodologies. Overall, while T. gondii whole-genome sequencing will be hardly feasible in most laboratories, this study shows that a discrete loci panel has the potential to improve the molecular epidemiology of T. gondii towards a better monitoring of circulating genotypes with clinical importance.