Desenvolvimento de metodologias de diagnóstico e caracterização molecular de Poliomavírus

Tese de mestrado. Biologia (Biologia Molecular Humana). Universidade de Lisboa, Faculdade de Ciências, 2009A família Polyomaviridae é composta por vírus de pequenas dimensões que, após infectarem o hospedeiro, permanecem em estado latente. No entanto, em situações de imunossupressão, têm capacidade de induzir sintomatologia e/ou doença no hospedeiro. O Poliomavírus JC (JCV), o Poliomavírus BK (BKV) e o Poliomavírus MC (MCV), encontram-se associados à Leucoencefalopatia Multifocal Progressiva, à Nefropatia Associada a Poliomavírus e ao Carcinoma das Células de Merkel, respectivamente. Relativamente aos Poliomavírus KI (KIV) e WU (WUV), ainda não foi estabelecido um papel etiológico. Devido à importância clínica do JCV e do BKV, bem como à necessidade de aprofundar o conhecimento sobre os novos Poliomavírus, é fundamental desenvolver e implementar metodologias sensíveis e específicas para o seu diagnóstico e caracterização molecular. Os objectivos deste trabalho foram o desenvolvimento e a optimização de metodologias de biologia molecular, para a detecção e quantificação destes vírus, bem como a caracterização molecular dos Poliomavírus JC e BK, de forma a determinar a proporção dos diferentes tipos circulantes. Foram desenvolvidas e validadas metodologias para a detecção do BKV (sensibilidade e especificidade de 100%), KIV, WUV e MCV e para a quantificação do JCV e do WUV (especificidade de 100% e sensibilidade na ordem das 10 cópias/μl). A caracterização molecular permitiu identificar, no caso do JCV, os tipos 1B, 2A, 2B, 3A e 4 e, no caso do BKV, os tipos Ib-1, Ib-2, II e IV. Os tipos mais prevalentes foram, respectivamente, o 1B (56,0%) e o II (62,5%). O desenvolvimento e a optimização de técnicas de biologia molecular para o diagnóstico e estudo dos Poliomavírus, assumem uma relevância particular, pois são métodos de diagnóstico não invasivos e com uma sensibilidade e especificidade superiores às dos métodos convencionais, nomeadamente da imagiologia, citologia e histologia. Simultaneamente, podem ser utilizados para o estudo da etiopatologia dos novos Poliomavírus.Polyomaviridae comprises small dimension viruses, which stay in a latent phase after primary infection. However, in immunossupressed individuals, they are able to induce symptoms and/or disease. JC polyomavirus (JCV), BK polyomavirus (BKV) and MC polyomavirus (MCV) are associated to Progressive Multifocal Leukoencephalopathy, to Polyomavirus-Associated Nephropathy and to Merkel Cell Carcinoma, respectively. An etiological role was not yet established for the KI and WU polyomavirus (KIV and WUV). Due to the JCV and BKV clinical relevance, as well as the need to extend the knowledge about the new polyomaviruses, it is crucial to develop and implement specific and sensitive methodologies for their diagnosis and molecular characterization. The main objectives of this study were the development and the optimization of methodologies for the detection and the quantification of these viruses, and the molecular characterization of JC and BK polyomaviruses. Methodologies for the detection of BKV, which had a sensitivity and a specificity of 100%, KIV, WUV and MCV were developed and validated, as well as the quantification of JCV and WUV (specificity of 100% and sensitivity of 10 copies/μl). Molecular characterization allowed the identification of the JCV types 1B, 2A, 2B, 3A and 4, and the BKV types Ib-1, Ib-2, II and IV. The most prevalent types were the 1B (56,0%) and the II (62,5%), respectively. The development and optimization of molecular methods for the polyomaviruses diagnosis and study have a particular relevance, since they are non-invasive diagnosis methods with higher sensitivity and specificity, comparing with conventional methods, like imagiology, cytology and histology. At the same time, they can be applied to etiopathogenicity studies of the new polyomaviruses

The cyclooxigenase-2 inhibitor parecoxib prevents epidermal dysplasia in HPV16-transgenic mice: efficacy and safety observations

Carcinogenesis induced by high-risk human papillomavirus (HPV) involves inflammatory phenomena, partially mediated by cyclooxigenase-2. In pre-clinical models of HPV-induced cancer, cyclooxygenase-2 inhibitors have shown significant e cacy, but also considerable toxicity. This study addresses the chemopreventive e ect and hepatic toxicity of a specific cyclooxigensase-2 inhibitor, parecoxib, in HPV16-transgenic mice. Forty-three 20 weeks-old female mice were divided into four groups: I (HPV16+/-, n = 10, parecoxib-treated); II (HPV16+/- n = 11, untreated); III (HPV16+/-, n = 11, parecoxib-treated) and IV (HPV16+/- n = 11, untreated). Parecoxib (5.0 mg/kg once daily) or vehicle was administered intraperitoneally for 22 consecutive days. Skin lesions were classified histologically. Toxicological endpoints included genotoxic parameters, hepatic oxidative stress, transaminases and histology. Parecoxib completely prevented the onset of epidermal dysplasia in HPV16+/- treated animals (0% versus 64% in HPV16+/- untreated, p = 0.027). Parecoxib decreases lipid peroxidation (LPO) and superoxide dismutase (SOD) activity and increases the GSH:GSSG ratio in HPV16+/- treated animals meaning that oxidative stress is lower. Parecoxib increased genotoxic stress parameters in wild-type and HPV16-transgenic mice, but didn’t modify histological or biochemical hepatic parameters. These results indicate that parecoxib has chemopreventive e ects against HPV16-induced lesions while maintaining an acceptable toxicological profile in this model.This work is supported by National Funds by FCT—Portuguese Foundation for Science and Technology, under the projects UID/AGR/04033/2019, UID/CVT/00772/2019 and UID/EQU/00511/2019 - Laboratory for Process Engineering, Environment, Biotechnology and Energy—LEPABE funded by national funds through FCT/MCTES (PIDDAC); Project “LEPABE-2-ECO-INNOVATION”—NORTE-01-0145-FEDER-000005, funded by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund.info:eu-repo/semantics/publishedVersio

Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance.

Klebsiella pneumoniae (Kp) bacteria are an increasing threat to public health and represent one of the most concerning pathogens involved in life-threatening infections and antimicrobial resistance (AMR). To understand the epidemiology of AMR of Kp in Portugal, we analysed whole genome sequencing, susceptibility testing and other meta data on 509 isolates collected nationwide from 16 hospitals and environmental settings between years 1980 and 2019. Predominant sequence types (STs) included ST15 (n = 161, 32%), ST147 (n = 36, 7%), ST14 (n = 26, 5%) or ST13 (n = 26, 5%), while 31% of isolates belonged to STs with fewer than 10 isolates. AMR testing revealed widespread resistance to aminoglycosides, fluoroquinolones, cephalosporins and carbapenems. The most common carbapenemase gene was blaKPC-3. Whilst the distribution of AMR linked plasmids appears uncorrelated with ST, their frequency has changed over time. Before year 2010, the dominant plasmid group was associated with the extended spectrum beta-lactamase gene blaCTX-M-15, but this group appears to have been displaced by another carrying the blaKPC-3 gene. Co-carriage of blaCTX-M and blaKPC-3 was uncommon. Our results from the largest genomics study of Kp in Portugal highlight the active transmission of strains with AMR genes and provide a baseline set of variants for future resistance monitoring and epidemiological studies

Detection of anti-infliximab antibodies is impacted by antibody titer, infliximab level and IgG4 antibodies: a systematic comparison of three different assays

Background: There is scant information on the accuracy of different assays used to measure anti-infliximab antibodies (ADAs), especially in the presence of detectable infliximab (IFX). We thus aimed to evaluate and compare three different assays for the detection of IFX and ADAs and to clarify the impact of the presence of circulating IFX on the accuracy of the ADA assays.Methods: Blood samples from 79 ulcerative colitis (UC) patients treated with infliximab were assessed for IFX levels and ADAs using three different assays: an in-house assay and two commercial kits, Immundiagnostik and Theradiag. Sera samples with ADAs and undetectable levels of IFX were spiked with exogenous IFX and analyzed for ADAs.Results: The three assays showed 81-96% agreement for the measured IFX level. However, the in-house assay and Immundiagnostik assays detected ADAs in 34 out of 79 samples, whereas Theradiag only detected ADAs in 24 samples. Samples negative for ADAs with Theradiag, but ADA-positive in both the in-house and Immundiagnostik assays, were positive for IFX or IgG4 ADAs. In spiking experiments, a low concentration of exogenous IFX (5 mu g/ml) hampered ADA detection with Theradiag in sera samples with ADA levels of between 3 and 10 mu g/ml. In the Immundiagnostik assay detection interference was only observed at concentrations of exogenous IFX higher than 30 mu g/ml. However, in samples with high levels of ADAs (> 25 mu g/ml) interference was only observed at IFX concentrations higher than 100 mu g/ml in all three assays. Binary (IFX/ADA) stratification of the results showed that IFX+/ADA and IFX-/ADAs + were less influenced by the assay results than the double-positive (IFX+/ADAs+) and double-negative (IFX-/ADAs-) combination.Conclusions: All three methodologies are equally suitable for measuring IFX levels. However, erroneous therapeutic decisions may occur when patients show double-negative (IFX-/ADAs) or double-positive (IFX+/ADAs+) status, since agreement between assays is significantly lower in these circumstances

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Effect of Conjugated Linoleic Acid on Memory and Reflex Maturation in Rats Treated During Early Life

In the critical period of neurodevelopment (gestation and lactation), maternal consumption of essential fatty acids (FAs) can alter the offspring cognitive function permanently causing damage. Lipids can regulate neurotrophin and compose brain tissue. However, the effects of maternal consumption of a mixture of conjugated linoleic acid (CLA) on an offspring nervous system are not completely clear. We aimed to investigate the impacts of different CLA concentrations mixed into the maternal diet during early life on neonatal reflex maturation and cognitive functions of the offspring. Three groups were formed: control (CG): receiving a standard diet; CLA1: receiving a diet containing 1% of CLA, and CLA3: receiving a diet containing 3% of CLA, offered during gestation and lactation. After birth, the reflex responses of the offspring were observed from the 1st to the 21st day. After weaning, the animals’ anxiety and memory were assessed using open field (OF) and novel object recognition tests. Fatty acids in the breast milk and the offspring’s brain were also quantified. The data were analyzed using one-way ANOVA and the Kruskal–Wallis test. CLA1 presented accelerated palmar grasp disappearance versus CLA3 and negative-geotaxis versus CG; and the CLA3 presented increases for most reflexes (cliff-avoidance, vibrissa-placing, negative-geotaxis, and auditory-startle response), and decrease in reflexes palmar grasp and free-fall righting versus CG (p < 0.05). CLA3 group explored less of the OF in the second exposure. CLA1 and CLA3 presented an increased exploration ratio for new objects, which indicates memory improvement. The milk tested from CLA3 demonstrated an increase in polyunsaturated fatty acids (PUFAs), and a decrease in monounsaturated fatty acids. The amount of CLA in milk was greater in CLA1 and CLA3 and in the brain offspring both presented moderated amounts of CLA. Maternal treatment with the CLA mixture induced anticipated reflex maturation and improved memory in the offspring. Even though CLA was detected in the brains in only trace amounts, offspring’s brain PUFA and SFA levels were increased. Further studies aimed to delineate the effect of maternal CLA supplementation on offspring’s brain lipid metabolism and long-term neurologic outcome are needed to confirm these findings

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery