Browsing by Author "Cochicho, Daniela"
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- 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.
- Collaborative study Brazil-Portugal - alidation of HPV lyophilized samples for the control of molecular testsPublication . Menezes, Maria Elizabeth; Fedrizzi, Edson Natal; Correa, José Abol; Cochicho, Daniela; Martins, Luís; Cunha, Mário; Ornelas, Carmo; Verdasca, Nuno; Faria, Ana PaulaThere are about 120 types of Human Papilloma Virus (HPV). The major importance about it is the oncogenic potential of some types. They are referred as a high and low risk for oncogenic potential. Given the importance of the disease it causes, and the use of different laboratorial techniques, mainly techniques of molecular biology, it is mandatory to have an External Quality Assurance (EQA) program base on harmonized standards that rely on consistent controls. The participation in EQA’s programs is mandatory in laboratorieswith an ISO 15189/17025 accreditation implemented. The control of Molecular Biology techniques is absolutely necessary for the quality assurance of the results, the tracking and monitorization of the performance of the reagents. However, one of its limitations is the stability, homogeneity of the material, (ISO/IEC 17043:2010 requisite) as well as the availability of control samples adequate for the parameter to be analyzed. The PNCQ, in order to fill this gap, lyophilised the HPV samples control. In order to do the validation and to test the reproducibility of these lyophilized samples, PNCQ sent to IBIOTECNO , INSA-PNAEQ -DDI and the IPOLFG-SPCLV to be analysed by different methods and reagents in two different countries and different laboratories.
- 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.
- Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin LymphomaPublication . Borges, Vítor; Isidro, Joana; Cunha, Mário; Cochicho, Daniela; Martins, Luís; Banha, Luís; Figueiredo, Margarida; Rebelo, Leonor; Trindade, Maria Céu; Duarte, Sílvia; Vieira, Luís; Alves, Maria João; Costa, Inês; Guiomar, Raquel; Santos, Madalena; Cortê-Real, Rita; Dias, André; Póvoas, Diana; Cabo, João; Figueiredo, Carlos; Manata, Maria José; Maltez, Fernando; Gomes da Silva, Maria; Gomes, João PauloRecent studies have shown that persistent SARS-CoV-2 infections in immunocompromised patients can trigger the accumulation of an unusual high number of mutations with potential relevance at both biological and epidemiological levels. Here, we report a case of an immunocompromised patient (non-Hodgkin lymphoma patient under immunosuppressive therapy) with a persistent SARS-CoV-2 infection (marked by intermittent positivity) over at least 6 months. Viral genome sequencing was performed at days 1, 164, and 171 to evaluate SARS-CoV-2 evolution. Among the 15 single-nucleotide polymorphisms (SNPs) (11 leading to amino acid alterations) and 3 deletions accumulated during this long-term infection, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus Spike protein. Although no convalescent plasma therapy was administered, some of the detected mutations have been independently reported in other chronically infected individuals, which supports a scenario of convergent adaptive evolution. This study shows that it is of the utmost relevance to monitor the SARS-CoV-2 evolution in immunocompromised individuals, not only to identify novel potentially adaptive mutations, but also to mitigate the risk of introducing "hyper-evolved" variants in the community.