Objetivos: O exercício físico regular em pacientes com fibrose cística (FC) auxilia no condicionamento aeróbico e diminui a progressão da doença, proporcionando melhor qualidade de vida. O objetivo desse estudo foi avaliar os efeitos de um programa de exercício físico aeróbico baseado na orientação verbal e instrumental na capacidade funcional e na qualidade de vida. Métodos: O Estudo constituiu-se de um ensaio clínico, randomizado, de orientações para o exercício físico realizado em um centro de FC. Os pacientes foram alocados em dois grupos, intervenção e controle, sendo 17 pacientes no grupo intervenção (G1) e 17 para o grupo controle (G2). A coleta de dados ocorreu durante o período de outubro de 2010 a outubro de 2011, e a população em estudo consistiu em crianças e adolescentes com FC e idade entre sete e 20 anos.A intervenção foi um manual de orientações com exercícios físicos aeróbicos e reforço das orientações por meio de contato telefônico a cada duas semanas. Resultados: Foram estudados 34 pacientes com FC, sendo que 20 pacientes (58,8)% eram do sexo masculino. Os grupos eram semelhantes no momento basal, sendo que no G1 seis pacientes (35,2%) referiram praticar exercício físico regularmente, a média de idade foi de 13,40±2,81 anos, do percentual do previsto do volume expiratório forçado no primeiro segundo (VEF1%) foi de 95,53±17,94 % e do consumo de oxigênio de pico relativo a massa corporal (VO2pico) foi de 34,93±9,09 ml/kg-1.min-1 . No G2, quatro pacientes (23,5%) referiram praticar exercício físico regularmente, a média de idade foi de 12,76±3,37 anos, do VEF1 foi de 100,13±21,27 % e do VO2pico foi de 33,21±8,26 ml/kg-1.min. Houve aumento significativo do G1 na prática de exercício físico relatada pelos pacientes após os três meses de intervenção comparado ao G2 (p=0,013). Nas demais variáveis não foram observadas diferenças estatisticamente significativas. Conclusão: Esse estudo demonstrou que a orientação verbal e instrumental para o exercício aeróbico, acoplado com supervisão telefônica teve impacto positivo no relato das crianças e adolescentes quanto a prática do exercício físico regular. Porém, não foram observados melhora nos parâmetros fisiológicos, nem nos domínios do questionário de qualidade de vida. / Objectives: Regular physical activity in patients with cystic fibrosis (CF) improves aerobic conditioning and delays disease progression, which results in better quality of life. This study evaluated the effect on functional capacity and quality of life of an aerobic physical activity program based on verbal and written guidelines. Methods: This randomized clinical trial used guidelines for physical exercise in a CF center. Patients were assigned to two groups: intervention (G1), with 17 patients; and control (G2), also with 17 patients. Data were collected from October 2010 to October 2011, and the study population comprised children and adolescents with CF aged 7 to 20 years. The intervention consisted of handing out a manual with guidelines for aerobic physical exercises and reinforcing recommendations in contacts by phone every two weeks. Results: Thirty-four patients were included in the study, 20 of whom were boys (58.5%). The groups were similar at baseline. In G1, 6 patients (35.2%) reported practicing physical exercises regularly; mean age was 13.40±2.81 years, mean percent predicted forced expiratory flow at one second (FEV1%) was 95.53±17.94% and mean peak oxygen uptake (VO2peak) relative to body mass was 34.93±9.09 ml/kg-1.min-1. In G2, four patients (23.5%) reported practicing physical exercises regularly. Mean age was 12.76±3.37 years, mean FEV1 was 100.13±21.27% and mean VO2peak was 33.21±8.26 ml/kg-1.min. In G1, there was a significant increase of physical exercise practice as reported by patients after three months of intervention when compared with G2 (p=0.013). No statistically significant differences were found for the other variables. Conclusion: Verbal and written guidelines for aerobic exercise, together with supervision over the phone, had a positive impact on the report of regular physical exercise practice by children and adolescents. However, no improvement was found in physiological parameters or domains of the quality of life questionnaire.

One of the most prevalent inherited diseases is cystic fibrosis. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. Generally, most of the prevalent mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). However, some mutations in nucleotide binding domain 2 (NBD2) can equally cause cystic fibrosis. In this work, a hierarchical graph is built for NBD2. Using this model for NBD2, we examine the consequence of single point mutations on NBD2. We collate the wildtype structure with eight of the most prevalent mutations and observe how the NBD2 is affected by each of these mutations.

Cystic Fibrosis (CF) is an autosomal recessive genetic disease that leads to severe malfunction in many organs, but particularly the lungs. The primary cause of this malfunction is the decrease of the airway surface liquid layer on the lung epithelium. The lack of hydration leads to mucus build up on the epithelial lining, leading to blockage of airways. The underlying cause of CF is the dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR), which results from mutations in the protein. Almost 90% of CF patients are caused by the deletion of the phenylalanine at position 508 of CFTR, which is believed to affect the folding and stability of CFTR. The misfolded ΔF508-CFTR undergoes ER associated degradation (ERAD), causing the failure of ΔF508-CFTR trafficking to the cell surface. Small molecule correctors yield moderate improvements in the trafficking of ΔF508-CFTR to the plasma membrane. It is currently not known if correctors increase trafficking through improved cargo loading of transport vesicles or through direct binding to CFTR. In this dissertation, real-time measurements of trafficking were utilized to identify the mechanistic details of chemical, biochemical, and thermal factors that impact CFTR correction, using the corrector molecule VX-809, a secondary mutation (I539T), and low temperature conditions. Each individually improved trafficking of ΔF508-CFTR to approximately 10% of wild-type levels. The combination of VX-809 with either low temperature or the I539T mutation increased the amount of CFTR on the plasma membrane to nearly 40%, indicating synergistic activity. The number of vesicles reaching the surface was significantly altered; however the amount of channel in each vesicle remained the same. Therefore, a 2 step therapeutic approach might be an ideal treatment for CF. The first step would be composed of a compound that mimics the mechanism of stabilization provided by low temperature or the I539T mutation, while the second step would be VX-809 or a similar corrector compound. These studies suggest that understanding how low temperature and second site suppressors alter ΔF508-CFTR could be key to the development of future therapeutics for the effective treatment of CF. The precise pathophysiology of cystic fibrosis is not well studied. The involvement of another transport protein, epithelial sodium channel (ENaC), makes the situation more complicated. ENaC and CFTR are colocalized on the apical surface of epithelia cells. With our fluorescence microscopy techniques, we explored the effects of CFTR on the residence time of ENaC on the cell membrane. A reliable approach measuring the half-life of protein on the cell membrane is required for this study. We present a new approach to quantify the half-life of membrane proteins on the cell surface, through tagging the protein with the photoconvertible fluorescent protein, Dendra2. Total internal reflection fluorescence microscopy (TIRF) is applied to limit visualization of fluorescence to proteins located on the plasma membrane. Photoconversion of Dendra2 works as a pulse chase experiment by monitoring only the population of protein that has been photoconverted. As the protein is endocytosed the red emission decreases due to the protein leaving the TIRF field of view. The half-life of the protein on the plasma membrane was calculated upon imaging over time and quantifying the change in red fluorescence. Our method provides a unique opportunity to observe real-time protein turnover at the single cell level without addition of protein synthesis inhibitors. This technique will be valuable for the future protein half-life study.

Glycosaminoglycans (GAGs) are linear polysaccharides whose disaccharide building blocks consist of an amino sugar and either uronic acid or galactose. They are expressed on virtually all mammalian cells, usually covalently attached to proteins, forming proteoglycans. GAGs are highly negatively charged due to an abundance of sulfate and carboxylic acid groups, and are structurally very diverse, with differences arising from chain length, the type of monomeric units, the linkages between each monomeric unit, the position of sulfate groups, and the degree of sulfation. GAGs are known to interact with a multitude of proteins, impacting diverse physiological and pathological processes. In addition, most of the biological interactions mediated by proteoglycans are believed to be primarily because of the GAG chains present on their surface. Considering the involvement of GAGs in multiple diseases, their use in the development of drugs has been of significant interest in the pharmaceutical field. Heparin, the first GAG-based drug developed in 1935, is still the most widely used anticoagulant in the world. The therapeutic potential of GAGs for the treatment of many other disease states, including cancer, inflammation, infection, wound healing, lung diseases, and Alzheimer’s disease, is being actively studied with many GAGs currently in clinical trials. However, challenges associated with the heterogeneous and complex structure of GAGs, limit their successful development. To combat such issues, our lab has focused on developing Non- Saccharide GAG Mimetics (NSGMs) as structural mimics of GAGs. NSGMs, being synthetic molecules, offer multiple advantages over GAGs. The studies mentioned here describe our efforts in the development of NSGMs as potential therapeutics for cancer, and cystic fibrosis.

Cystic Fibrosis (CF) is a lethal autosomal recessive genetic disorder caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR transports anions at the apical surface of epithelial membranes and functions in many areas of the body. However in CF, loss of CFTR function in the lungs is the major source of morbidity and mortality. Replacing the defective CFTR in the lungs through gene therapy has the potential to cure the disease. Recombinant adeno-associated virus (AAV) is an effective gene transfer vector and has been used extensively to deliver genes to cells in culture. A number of clinical trials using AAV have been attempted for a variety of diseases, including CF, albeit with limited success. Poor vector transduction efficiency prevents effective gene therapy. We have previously used a technique to greatly increase the transduction efficiency of AAV in human lung tissues by selecting from a library of AAVs using a directed evolution technique. However, this evolution was performed in cultured cells and did not fully represent the in vivo environment in which the AAV would be used. In 2008, a CF pig model was developed to develop a further understanding of the mechanisms of CF and CFTR function. We hypothesized that we could use directed evolution to select for a vector in vivo using the pig, allowing gene therapy studies to be conducted in a physiologically relevant model of CF. We selected a novel AAV variant, called AAV2H22, which is closely related to AAV2 but with greatly increased transduction efficiency in pig airway epithelia. AAV2H22 displayed specific tropism for pig airway epithelia and saturated cell surface receptors, indicating specific binding in those cells. We found that AAV2H22-mediated gene transfer corrected chloride and bicarbonate transport defects both in vitro and in vivo. Importantly, bicarbonate transport was sufficient to normalize pH in the airway surface liquid, resulting in increased bacterial killing likely due to increased activity of antimicrobial peptides. To investigate the mechanics of the increased transduction of AAV2H22, capsid mutants were assayed for transduction efficiency. Two of the five amino acid differences between AAV2 and AAV2H22 lie at the surface and are predicted to alter capsid binding. This is consistent with the results showing specific binding in cultured airway epithelia. This research has important implications for gene therapy and investigations using AAV2H22 will increase our understanding of the biology needed to successfully treat CF.

Notre génome contient des centaines de milliers de variants génétiques, qui pour la plupart, n’ont aucun impact sur notre santé. Après séquençage, il faut les filtrer pour ne conserver que ceux qui sont potentiellement impliquées dans une maladie. On utilise des annotateurs qui prédisent l’impact des variants. Ces prédictions sont faites sans tenir compte des variants en cis dans le même gène. Pourtant, des variants neutres peuvent, lorsqu’ils sont réunis chez un individu, devenir délétères. J’ai donc développé l’outil bioinformatique GEMPROT qui permet de visualiser l’effet des variants génétiques sur la séquence protéique et de mettre en évidence les combinaisons de variants touchant un même domaine fonctionnel.J’ai ensuite étudié l’impact de deux variants associés à la p.Phe508del (508del) sur la protéine CFTR.Le variant p.Val470M est présent sur tous les haplotypes portant la délétion mais pas sur la séquence de référence, qui est généralement utilisée pour la construction de plasmides. Nous avons montré des différences de fonction de la protéine CFTR selon l’acide aminé en position 470. La fonction est augmentée avec une Valine et il convient donc de s’assurer, lors de la construction de plasmides, que le contexte haplotypique des variants étudiés est bien respecté. Le variant p.Ile1027Thr conduit à une dégradation de la fonction de la protéine 508del.Ce variant n’est présent que sur une partie des haplotypes 508del et pourrait donc avoir un effet modificateur de l’expression de la délétion. En conclusion, nous montrons l’importance de la prise en compte des contextes haplotypiques dans l’étude des maladies et proposons un outil bioinformatique pour le faire. / We all carry hundreds of thousands genetic variations in our genome that, for the most of them, have no impact on our health. After sequencing, they must be filtered to only retain those potentially involved in a disease. We use annotators that predict the impact of variants.These predictions are done for each variant taken independently without considering cis variants in the same gene. However, neutral variants can become deleterious when associated together. I have developed the bioinformatics tool GEMPROT, which makes it possible to visualize the effect of genetic variants on the protein sequence and to highlight combinations of variants affecting the same functional domain.I then studied the impact of two variants associated with p.Phe508del (508del) on CFTR protein function.The variant p.Val470M is present on all carrying deletion haplotypes but not on the reference sequence, which is generally used for the construction of plasmids. We have shown differences in the function of the mutated CFTR protein 508del according to the amino acid at position 470. The function is increased with a Valine and it is therefore necessary to ensure, when constructing plasmids, that the haplotype context of the studied variants is well respected.The variant p.Ile1027Thr leads to a degradation of the function of the 508del protein. This variant is present only on a portion of the 508del haplotypes and could therefore have a modifying effect on deletion expression. In conclusion, we show the importance of considering haplotype contexts in the diseases studies and propose a bioinformatics tool to do so.

<p>Immunoglobulin Y (IgY) is the major antibody found in eggs from chicken (Gallus domesticus). IgY can be used as an alternative to mammalian antibodies normally used in research, and its use in immunotherapy has recently been proposed. Compared to mammalian antibodies, IgY possesses several biochemical advantages and its simple purification from egg yolk prevents a stressful moment in animal handling, as no bleeding is necessary. </p><p>Small amount of antigen (1 mg) can be used to elicit an immune response in chickens and there are low intra-individual differences regarding antibody concentration found in yolk. By studying two chicken breeds and their cross, a genetic correlation was shown regarding the IgY concentration, which implies a possibility by breeding to increase IgY concentrations. By using IgY instead of goat antibody as capture antibody in ELISA, it is possible reduce interferences by complement activation. After oral administration of IgY to healthy volunteers, IgY activity was present in saliva 8 hours later, indicating a protective effect. This effect has been studied in an open clinical trial with cystic fibrosis patients. Specific IgY against Pseudomonas aeruginosa given orally prolongs the time of intermittent colonization by six months, decrease the number of positive colonizations and might be a useful complement to antibiotic treatment. Immunoglobulin therapy may diminish the development of antibiotic resistant microorganisms. The use of immunoglobulin therapy broadens the arsenal available to combat pathogens in medicine and IgY is a promising candidate, both as an alternative to antibiotics and as a useful tool in research and diagnostics.</p>

<p>S-nitrosogluthatione is an endogenous substance, present at decreased levels in the lungs of CF patients and was recently found to induce mature CFTR in airway epithelial CF cell lines. We show that S-nitrosoglutathione in physiological concentrations increases the presence of ΔF508 CFTR in the cell membrane and induces cAMP dependent chloride transport in cystic fibrosis airway epithelial cells. The properties of S-nitrosoglutathione include other potential benefits for the CF patient and make this agent an interesting candidate for pharmacological treatment of CF that needs to be further evaluated.</p><p>Genistein was found to increase the chloride efflux in both normal and ΔF508 cells without stimulation of cAMP elevating agents and without prior treatment with phenylbutyrate. Genistein, in concentrations close to those that can be detected in plasma after a high soy diet, could induce chloride efflux in cells with the ΔF508 CFTR mutation and its possible use in the treatment of CF should therefore be further investigated.</p><p>Studies on nasal epithelial cells from CF patients showed cAMP dependent chloride efflux in some of the patients with severe genotypes. This may complicate <i>in vitro</i> evaluation of clinical treatment of these patients. The presence of cAMP dependent chloride transport did not necessarily lead to a milder phenotype. Other factors than CFTR may influence the clinical development of the disease.</p><p>Cystic fibrosis (CF) is the most common monogenetic disease among Caucasians. A defective cAMP regulated chloride channel (cystic fibrosis transmembrane conductance regulator, CFTR) in epithelial cells leads to viscous mucus, bacterial infections, inflammation and tissue damage in the lungs that cause death in 95% of the cystic fibrosis patients. There is no cure for the disease although existing treatment has dramatically prolonged the life expectancy. The aim of this thesis was to study pharmacological agents for their ability to restore the cellular deficiency in CF airway epithelial cells. X-ray microanalysis, MQAE fluorescence and immunocytochemistry were used to evaluate the effects.</p>

<p>Cystic fibrosis (CF) is the most common lethal genetic disease in the white population. It is due to mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR), a protein that functions mainly as a cAMP-activated chloride channel. The disease impairs ion and water transport in epithelia-lined organs such as airways, digestive tract, reproductive epithelium and sweat glands. At present the only therapy is symptomatic and development of curative treatment depends on uncovering the links between the defective CFTR and the disease, as well as on improving end-point measurements. </p><p>A method has been established for studying ion transport in an easily accessible cell type (nasal epithelial cells) from normal and cystic fibrosis patients by X-ray microanalysis. This method represents a rather simple and direct way of measuring simultaneously several chemical elements of biological interest.</p><p>Studies of chloride transport by means of a fluorescent indicator (MQAE) in nasal epithelial cells from CF patients showed that the phenotype cannot exclusively be explained by the CFTR activity in patients with severe genotype. </p><p>A common Portuguese CFTR mutation (A561E) causes protein mislocalization in the endoplasmic reticulum similar to the most common CF mutation (ΔF508) and thus it should be possible to treat it with the same pharmacological strategies.</p><p>Chronic treatment of CF airway epithelial cells with nanomolar concentrations of colchicine increased the chloride efflux via chloride channels other than CFTR, strengthening the notion that colchicine could be beneficial to CF patients.</p><p>Successful <i>in vitro </i>transfection of CF airway epithelial cells with cationic vectors was possible with short incubation times. Heparin added at the end of the transfection incubation time could help to maintain the viability of the cells, without interfering with the transfection efficiency. It seems possible that heparin could be an adjuvant for non-viral mediated gene therapy.</p>

Immunoglobulin Y (IgY) is the major antibody found in eggs from chicken (Gallus domesticus). IgY can be used as an alternative to mammalian antibodies normally used in research, and its use in immunotherapy has recently been proposed. Compared to mammalian antibodies, IgY possesses several biochemical advantages and its simple purification from egg yolk prevents a stressful moment in animal handling, as no bleeding is necessary. Small amount of antigen (1 mg) can be used to elicit an immune response in chickens and there are low intra-individual differences regarding antibody concentration found in yolk. By studying two chicken breeds and their cross, a genetic correlation was shown regarding the IgY concentration, which implies a possibility by breeding to increase IgY concentrations. By using IgY instead of goat antibody as capture antibody in ELISA, it is possible reduce interferences by complement activation. After oral administration of IgY to healthy volunteers, IgY activity was present in saliva 8 hours later, indicating a protective effect. This effect has been studied in an open clinical trial with cystic fibrosis patients. Specific IgY against Pseudomonas aeruginosa given orally prolongs the time of intermittent colonization by six months, decrease the number of positive colonizations and might be a useful complement to antibiotic treatment. Immunoglobulin therapy may diminish the development of antibiotic resistant microorganisms. The use of immunoglobulin therapy broadens the arsenal available to combat pathogens in medicine and IgY is a promising candidate, both as an alternative to antibiotics and as a useful tool in research and diagnostics.