La mucoviscidose (CF) est causée par des mutations sur le gène CFTR codant pour une protéine indispensable au maintien de l'homéostasie des transports hydro-électrolytiques au sein de l'épithélium des organes cibles de la pathologie, dérivés de l'endoderme (poumon, pancréas, appareil reproducteur). Entre ces différents tissus et au cours du développement fœtal, l'expression du gène varie, particulièrement dans le tissu pulmonaire où une répression est observée à l'âge adulte.Ce travail propose dans une première partie la caractérisation des modifications épigénétiques associées à la régulation spatio-temporelle physiologique de l'expression du gène CFTR dans les tissus humains sains adultes et fœtaux. Les résultats obtenus soulignent le rôle important des modifications post-traductionnelles des histones dans la régulation in vivo. Nous avons notamment observé i) un équilibre fin entre marques d'ouverture (acétylation) et de fermeture (H3K27Me3) de la chromatine sur la région promotrice du gène CFTR et ii) l'acétylation significative de régions cis-régulatrices intragéniques.La deuxième partie de ce travail consiste en l'évaluation des effets du SAHA, un inhibiteur d'histones déacétylases (HDACi) dans un modèle ex vivo d'épithélium nasal de patients atteints de mucoviscidose. Les résultats montrent que le SAHA ne restaure pas l'adressage membranaire de la protéine CFTR en contexte pathologique mucoviscidose (mutation p.(Phe508del)) dans des cellules CF différenciées en épithélium ex vivo. De plus, le SAHA induit une modification du profil inflammatoire des épithélia et une dé-différenciation épithéliale dans le modèle ex vivo montrant que les mécanismes d'action de cette molécule sont multiples et réversibles.Ce travail souligne la nécessité d'analyser in vivo les mécanismes physiopathologiques impliqués dans la mucoviscidose et d'évaluer l'impact des molécules thérapeutiques sur les protéines endogènes dans un modèle d'épithélium différencié. / Cystic fibrosis (CF) is caused by mutations in the CFTR gene encoding for a protein essential to maintain the homeostasis of fluid and electrolyte transport in the epithelium of endoderm-derived organs (lung, pancreas, reproductive tract) that are affected in CF patients. CFTR expression greatly varies between these tissues and during fetal development, particularly in the lung where repression is observed in adulthood .In the first part of this work, we characterized epigenetic modifications associated with the spatio-temporal regulation of CFTR gene expression in healthy human adult and fetal tissues. Our results emphasize the important role of histone post-translational modifications in this regulation in vivo. Specifically, we observed i) a fine balance between active (acetylation) and repressive (H3K27Me3) marks in the promoter region and ii) significant acetylation in intragenic cis-regulatory regions.In the second part of this work, we evaluated the effects of SAHA, a histone deacetylase inhibitor (HDACi) in an ex vivo model of nasal epithelium of CF patients. Our results show that SAHA can not restore CFTR protein to the apical membrane in a p.(Phe508del)-CFTR context in ex vivo CF differentiated epithelial cells. In addition, SAHA induces a change in the inflammatory profile of epithelia and epithelial dedifferentiation in the ex vivo model showing that the mechanisms of action of this molecule are multiple and reversible.This work highlights the need to analyze in vivo the pathophysiological mechanisms involved in Cystic Fibrosis and to evaluate the impact of therapeutic molecules on the endogenous proteins in a differentiated epithelium model.

La première partie de ce travail se centre sur la recherche de tests sanguins (reposant sur les granulocytes) de dépistage, de suivi et d’efficacité thérapeutique dans différentes maladies allergiques. Elle débute par un travail réalisé dans la maladie asthmatique. Elle se poursuit par l’étude du rôle des granulocytes (polynucléaires neutrophiles et/ou polynucléaires éosinophiles et/ou basophiles) dans deux maladies allergiques : l’oesophagite à éosinophiles et les allergies alimentaires. Chez des patients atteints d’oesophagite à éosinophiles, nous avons étudier le profil d’activation des éosinophiles sanguins et de l’œsophage. Nous nous sommes focalisés sur certains marqueurs d’activation de surface (CD66b) et sur certains phosphoépitopes d’intérêt (Ph-STAT1 et Ph-STAT6). Nous avons démontré que les éosinophiles sanguins avaient un profil spécifique dans cette maladie. Enfin, cette première partie s’achève par deux études portant sur les basophiles sanguins dans les allergies alimentaires, plus précisément, dans les allergies aux fruits à coques ; Nous avons développé de nouveaux potentiels tests de dépistage de patients atteints d’allergies alimentaires, d’identification des allergènes responsables ainsi que de potentiels marqueurs d’évaluation d’efficacité de nouvelles thérapeutiques dans les allergies alimentaires par l’utilisation des marqueurs d’activation de surface des basophiles.La deuxième partie se centre principalement sur le rôle des polynucléaires neutrophiles (PNN) du sang et des voies aériennes des patients atteints de mucoviscidose. La mucoviscidose est la maladie génétique autosomique récessive la plus fréquente dans l’Europe du nord. Son pronostic est étroitement lié à l’atteinte pulmonaire, qui se caractérise par des infections à répétition, une obstruction et une inflammation à PNN. Notre équipe a tout d’abord démontré que les PNN sanguins de patients atteints de mucoviscidose présentaient un déficit en glutathion. Nous avons donc réaliser un essai clinique de phase IIa ou, N-acétyl-cystéine (précurseur du glutathion) était donné, à forte dose et par voie orale à des patients atteints de mucoviscidose. Ce traitement par N-acétyl-cystéine pendant douze semaines a permis une correction du déficit des PNN sanguins en glutathion. Cette correction de l’excès de stress oxydatif au sein des PNN a permis une diminution significative du nombre d’exacerbation chez les patients atteints de mucoviscidose. En revanche, possiblement en raison de la courte durée de ce traitement, aucune différence significative ne fut observée au niveau des paramètres de fonction respiratoire, tels que le VEMS. De plus, nous avons démontré que les PNN des voies aériennes des patients atteints de mucoviscidose dysfonctionnaient. En effet, alors qu’il était rapporté dans la littérature que les PNN nécrotiques des voies aériennes larguaient de manière passive l’élastase et la myélopéroxidase, nous avons démontré que les PNN vivants larguaient de manière active ces deux enzymes, dont la présence est en étroite corrélation avec le déclin de la fonction pulmonaire.. Nous avons alors émis l’hypothèse que les PNN, lors de leur migration du sang vers les voies aériennes, s’activaient anormalement. Nous avons donc décider d’étudier leurs cascade d’activations intracellulaire. Nous avons ainsi démontré que les PNN des voies aériennes des patients atteints de mucoviscidose présentaient une régulation positive de la voie mTOR. mTOR étaient possiblement activé par la pléthore d’acides aminés présents dans le poumon mucoviscidosique. mTOR pourrait refléter une possible survie prolongée des PNN des voies aériennes du poumon mucoviscidosique. Ces PNN pourraient aussi secréter de nouvelles protéines, alors même qu’ils sont « conventionnellement » définis comme cellules terminallement différenciées. [...] / Summary of the first part. We hypothesized that granulocytes were not only playing an effector role in atopic diseases, but also a regulatory role. Furthermore, we proposed that granulocytes, due to their rapid activation response, could be used in rapid non-invasive whole blood assays for Allergic Asthma (AA), Food Allergy (FA) and Eosinophillic Esophagitis (EoE), three allergic diseases. We first studied asthma. Then, we explored the profil of activation of blood eosinophils in patients with EoE. We explored some activation surface markers (CD66b) and some intracellular phosphoepitopes of interest (Ph-STAT1 and Ph-STAT6). We then focused our attention on blood basophils in food allergy. We developped a potential blood basophil assay (based on two basophil activation surface markers, CD203c and CD63), which could discriminate a patient with food allergy, which could also identify the offending allergen and, which could monitor the effect of new therapy.Summary of the second part. We focused our attention on the role of the blood and sputum neutrophils in cystic fibrosis (CF). Cystic fibrosis is the most frequent disease in Caucasians. While CF affects all exocrine organs throughout the body, its lung manifestation represents the main cause of morbidity and mortality. We first discovered that blood neutrophils were deficient in glutathion. We therefore started a clinical phase IIa, where N-acetyl-cystein were given orally in high dose to patients with CF for twelve weeks. Thanks to this regimen, the deficit in glutathion in blood PNN disappeared. The number of exacerbations significantly decreased, however, no positive effect were observerd on the lung function. Furthermore, we demonstrated that profound functional and signaling changes readily occur within viable PNN recruited to CF airways, compared to their blood counterparts. For a long time, neutrophil dysfunction in CF airways has been equated with necrosis and passive release of elastase, DNA and, actin. However, we established recently by direct ex vivo analysis of airway neutrophils from CF patients that a large fraction of these cells are viable and appear to actively release these enzymes-containing granules. We also show that neutrophils that entered CF airways have increased phosphorylation of key effectors in the amino acid-regulated mammalian target of rapamycin (mTOR) pathway. An upregulation of the mTOR pathway might reflect an increase of the survival of the neutrophils in the airways. Another common view of peripheral neutrophils is that of terminally differentiated population, with little if any ability to become anabolic. However, we outlined the ability of human neutrophils to modify their transcriptional profile upon migration to the lung in CF. The last part of these thesis is a combination of knowledge that we acquired on the blood basophils in food allergy and on the neutrophils from the airways of patients with CF. We are currently trying to develop an unmet need blood (basophil) test which could discrimate the CF patients with allergic bronchopulmonary aspergillosis. We are also trying to understand the role of airways neutrophils and eosinophils in the pathogenese of these disease.

Doctor of Philosophy / Department of Anatomy and Physiology / Bruce Schultz / Transforming growth factor β1 (TGF-β1) is a cytokine that reportedly affects the severity of cystic fibrosis lung disease. The goal of this project was to define the effect of TGF-β1 on vas deferens, an organ that is universally affected in male cystic fibrosis patients. In the first study, experiments were conducted using freshly isolated porcine vas deferens epithelial cells. Primary porcine vas deferens epithelial cells exposed to TGF-β1 exhibited a significantly reduced basal transepithelial electrical resistance (Rte). TGF-β1-induced reduction in Rte was prevented by SB431542, a TGF-β receptor I inhibitor, indicating that the effect of TGF-β1 requires the activation of TGF-β receptor I. Western blot and immunohistochemistry results showed the expression of TGF-β receptor I in native vas deferens epithelia, indicating that the impaired barrier function and anion secretion that were observed in cultured vas deferens cells can likely be observed in the native context. Immunohistochemical outcomes showed that TGF-β1 exposure led to loss of organization of tight junction proteins occludin and claudin-7. These outcomes suggest that TGF-β1 impairs the barrier integrity of epithelial cells lining the vas deferens. In a parallel study that employed PVD9902 cells that are derived from porcine vas deferens, TGF-β1 exposure significantly reduced anion secretion stimulated by forskolin, forskolin/IBMX, and 8-pCPT-cAMP, suggesting that TGF-β1 affects downstream targets of the cAMP signaling pathway. Real-time RT-PCR and western blot analysis showed that TGF-β1 exposure reduced both the mRNA and the protein abundance of cystic fibrosis transmembrane conductance regulator (CFTR). Pharmacological studies showed that the inhibitory effect of TGF-β1 on forskolin-stimulated anion secretion was abrogated by SB431542 and attenuated by SB203580, a p38 mitogen-activated protein kinase (MAPK) inhibitor. These outcomes suggest that TGF-β1, via the activation of TGF-β receptor I and p38 MAPK signaling, reduces CFTR expression, and thus impairs CFTR-mediated anion secretion. Outcomes from these studies suggest that, in epithelial cells lining the vas deferens, TGF-β1 exposure leads to an impaired physical barrier and/or reduced anion secretion, which is expected to modify the composition and the maintenance of the luminal environment and thus, is expected to reduce male fertility.

Doctor of Philosophy / Department of Biochemistry / John M. Tomich / Channel replacement therapy represents a new treatment modality that could augment existing therapies against cystic fibrosis. It is based on designing synthetic channel-forming peptides (CFPs) with desirable selectivity, high ion transport rates and overall ability to supersede defective endogenous chloride channels. We derived synthetic CFPs from a peptide initially reconstituted from the second transmembrane segment of the α-subunit of Glycine receptor (M2GlyR). Our best candidate peptide NK4-M2GlyR T19R, S22W (p22-T19R, S22W) is soluble in aqueous solutions, has the ability to deliver itself to the epithelial cell membranes without the use of a delivery system, is non-immunogenic, but when assembled into a pore, lacks the structural properties for anion selectivity. Previous findings suggested that threonine residues at positions 13, 17 and 20 line the pore of assembled p22-T19R, S22W and recent studies indicated that an introduction of positively charged 2, 3-diaminopropionic acid (Dap) at either T13 or T17 in the sequence increases transepithelial ion transport rates across the apical membranes of Madin-Darby canine kidney (MDCK) epithelial cells. This study focused on further structural modifications of the pore-lining interface of p22-T19R, S22W assembled pore. It was hypothesized that singly, doubly or triply introduced Dap residues modify the pore geometry and that their positively charged side chains impact discrimination for anions. Dap-substituted p22-T19R, S22W peptides retain the α-helical secondary structure characteristic for their parent p22-T19R, S22W. The sequences containing multiple Dap-substituted residues induce higher short circuit current across the epithelial MDCK cells compared to peptides with single Dap-substitutions or no Dap-substitutions. Whole-cell voltage clamp recordings using Xenopus oocytes indicate that Dap-substituted peptide assemblies induce higher levels of voltage-dependent but non-selective ion current relative to p22-T19R, S22W. Studies using the D-enantiomer of p22-T19R, S22W and shorter truncated sequences of a full length L-p22-T19R, S22W and L-Dap-substituted peptides provided evidence that peptide-induced ion transport rates can be attributed to formation of de novo pathways. Results of preliminary computer modeling studies indicate that Dap residues affect the pore geometry but not ion selectivity. Future studies focusing on modifying the existing electrostatic environment towards anion selectivity will focus on staggering the charged residues of Dap at various locations inside synthetic pores.

<p>Proteins are essential components of cells and are crucial for catalyzing reactions, signaling, recognition, motility, recycling, and structural stability. This diversity of function suggests that nature is only scratching the surface of protein functional space. Protein function is determined by structure, which in turn is determined predominantly by amino acid sequence. Protein design aims to explore protein sequence and conformational space to design novel proteins with new or improved function. The vast number of possible protein sequences makes exploring the space a challenging problem. </p><p>Computational structure-based protein design (CSPD) allows for the rational design of proteins. Because of the large search space, CSPD methods must balance search accuracy and modeling simplifications. We have developed algorithms that allow for the accurate and efficient search of protein conformational space. Specifically, we focus on algorithms that maintain provability, account for protein flexibility, and use ensemble-based rankings. We present several novel algorithms for incorporating improved flexibility into CSPD with continuous rotamers. We applied these algorithms to two biomedically important design problems. We designed peptide inhibitors of the cystic fibrosis agonist CAL that were able to restore function of the vital cystic fibrosis protein CFTR. We also designed improved HIV antibodies and nanobodies to combat HIV infections.</p> / Dissertation

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene (CF transmembrane conductance regulator). These mutations result in absent or defective CFTR chloride channel function. The susceptibility to bacterial respiratory infections due to the accumulation of thickened mucus and altered glycosylation in lungs is typical for this disease. Bacteria Pseudomonas aeruginosa (PA) is a major cause of these infections. Among other virulent factors, the pathogenicity of these bacteria is caused by fucose-specific PA-IIL lectin which plays a role as an adhesin. The effect of anti-PA-IIL egg yolk antibodies and multivalent fucose-based PA-IIL inhibitors on PA adherence to lung epithelial cells was studied in this work. Chicken antibodies were isolated from egg yolks before and after immunization with antigen PA-IIL. Specific anti-PA-IIL antibodies were obtained by affinity chromatography using a column with an immobilized PA-IIL. Reactivity of IgY was verified by ELISA. The presence of PA-IIL in the bacterial culture of Pseudomonas aeruginosa (PAK, ST 1763) and the ability of antibodies to recognize this bacterial lectin were verified by Western blotting followed by immunodetection. Appropriate culture conditions have also been found for the expression of this lectin. The...

Introdução: a fibrose cística é uma doença crônica, multissistêmica, autossômica recessiva, de caráter genético. A expectativa de vida de quem convive com essa doença tem aumentado com os avanços no tratamento e com o controle das infecções. Por isso, o número de pessoas que chegam à idade adulta vem crescendo, o que faz surgirem novas demandas de atenção. Objetivo: compreender a experiência de pessoas adultas que convivem com a fibrose cística. Método: trata-se de um estudo qualitativo fundamentado na fenomenologia social de Alfred Schütz, realizado com doze pessoas adultas, que possuíam fibrose cística, residentes na cidade de São Paulo. Para obtenção dos depoimentos, utilizou-se a entrevista fenomenológica, com as seguintes questões norteadoras: como é para você conviver com a fibrose cística? Considerando que você tem essa doença crônica, quais são seus planos para o futuro? A Fenomenologia Social de Alfred Schütz permitiu a organização e a análise dos resultados. A discussão do conjunto de categorias que emergiram da experiência vivida foi realizada com base na literatura temática, tendo como fio condutor o referencial teórico-metodológico adotado. O projeto foi aprovado pelo Comitê de Ética em Pesquisa com seres humanos da Escola de Enfermagem da Universidade de São Paulo, sob o Parecer nº 1.400.118. Resultados: o grupo de adultos com fibrose cística é aquele que convive com a doença e seu impacto desde a infância/adolescência, fases estas que foram representativas para eles, pois foi o momento em que os sintomas iniciaram e eles se perceberam diferentes dos colegas. As pessoas que fazem parte desse grupo social lidam com o preconceito e com o constrangimento causados pelos sinais e sintomas como a fadiga respiratória, a tosse e ainda o tratamento da doença, o que dificulta a realização das atividades cotidianas. Apesar das dificuldades de conviver com a fibrose cística, eles se mostram resilientes, otimistas e adaptam a rotina de tratamento ao seu cotidiano. No que tange ao futuro, os participantes deste estudo referem o medo da morte. No entanto referem-se ao transplante pulmonar como possibilidade de melhorar a qualidade de vida, isto é, estar livres da rotina rígida do tratamento, ter autonomia, independência, além de poder constituir família, dar continuidade aos estudos, conseguir um emprego e realizar atividades que lhes dão prazer. Conclusões: a fenomenologia social de Alfred Schütz possibilitou compreender a experiência de adultos com fibrose cística no contexto social onde estão inseridos, evidenciando elementos importantes para a elaboração de estratégias de cuidado centradas nas necessidades reais deste grupo. Essas necessidades devem ser refletidas no âmbito assistencial, do ensino e da pesquisa em saúde. / Introduction: Cystic fibrosis is a chronic, multisystem, autosomal recessive, genetic disease. The life expectancy of those living with this disease has increased with advances in treatment and control of infections. Therefore, the number of people who reach adulthood has been increasing, which brings new demands for attention. Objective: to understand the experience of adults living with cystic fibrosis. Method: This is a qualitative study based on the social phenomenology of Alfred Schütz, carried out with twelve adults, who had cystic fibrosis living in the city of São Paulo. To obtain the depositions, the phenomenological interview was used, with the following guiding questions: How do you cope with cystic fibrosis? Considering that you have this chronic disease, what are your plans for the future? The Social Phenomenology of Alfred Schütz allowed the organization and analysis of the results. The discussion of the set of categories that emerged from the lived experience was carried out based on the thematic literature, having as a guiding thread the theoretical-methodological reference adopted. The project was approved by the Committee of Ethics in Research with human beings of the School of Nursing of the University of São Paulo, under Opinion no. 1,400,118. Results: group of adults with cystic fibrosis is the one who lives with the disease and its impact since childhood / adolescence, these phases were representative for them, because it was that moment that the symptoms started and they perceived different from their colleagues. People who are part of this social group deal with the prejudice and the embarrassment caused by signs and symptoms such as respiratory fatigue, coughing and even treatment of the disease, which makes it difficult to perform daily activities. Despite the difficulties of living with cystic fibrosis, they are resilient, optimistic and adapt the routine of treatment to their daily lives. When thinking about the future, people with cystic fibrosis refer to the fear of death, but refer to lung transplantation as a possibility to improve the quality of life, that is, to be free of the rigid routine of treatment, to have autonomy, independence and be able to start a family, continue their studies, get a job and perform activities that give them pleasure. Conclusions: the social phenomenology of Alfred Schultz made it possible to understand the experience of adults with cystic fibrosis in the social context where they are inserted, showing important elements for the elaboration of care strategies focused on the real needs of this group. These needs must be reflected in the healthcare, teaching and health research.

Fibrose cística é uma doença hereditária, caracterizada por alterações no transporte de cloro nas membranas das células epiteliais, gerando a produção de muco espesso e anormal, o que pode obstruir os ductos de glândulas exócrinas de vários órgãos. As manifestações clínicas principais da doença abrangem os sistemas respiratório (com infecções pulmonares recorrentes e crônicas) e gastrointestinal (com insuficiência pancreática e consequente má-digestão e absorção de nutrientes, levando a desnutrição energético-protéica). Existem evidências de que a constituição da microbiota intestinal pode influenciar a colonização do trato respiratório de indivíduos com fibrose cística. Esta dissertação teve como objetivo realizar revisão sistemática e metanálise das publicações científicas sobre o uso de pré, pró ou simbióticos em fibrose cística, além de avaliar a situação nutricional dos pacientes com fibrose cística acompanhados no Instituto da Criança - HCFMUSP. A revisão sistemática e metanálise seguiu protocolo proposto pela Colaboração Cochrane, com buscas em bases de dados eletrônicas com os termos prebioticos ou probióticos ou simbióticos e fibrose cística. Foram incluídos ensaios clínicos randomizados que abordassem os desfechos de inflamação intestinal e/ou exacerbações pulmonares. O estudo de avaliação nutricional foi realizado através de levantamento de dados antropométricos e clínicos, além de questionários aplicados a pacientes e responsáveis sobre dados de consumo alimentar e características socioeconômicas. Na busca bibliográfica foram encontrados 48 diferentes estudos, e somente 6 atingiram os critérios para integrar a metanálise. Foi observado efeito protetor do uso de probióticos e simbióticos na taxa de exacerbação pulmonar em pacientes com fibrose cística quando comparados com placebo (OR= -1,01 (IC 95% -1,66; -0,37), p = 0,002). Os níveis de calprotectina fecal (indicador de inflamação intestinal) tiveram redução significativa após intervenção (OR= -12,18 (IC 95%: -22,50; -1,86), p = 0,02), e houve diminuição dos pacientes com inflamação intestinal (calprotectina > 50 mcg/g de fezes) com OR= 0,31 (IC 95%: 0,13; 0,79), p = 0,01. Na avaliação do perfil nutricional foram incluídos 101 pacientes (59,4% do gênero masculino, 86,4% caucasianos), e a mediana de idade na inclusão foi de 10 anos. A maioria dos pacientes foi classificada como eutrófica, com consumo alimentar adequado. Valores menores de escore Z de IMC foram observados em escolares e adolescentes, e a proporção de pacientes com peso abaixo do esperado aumenta de 10% entre pré-escolares para 35% na faixa etária escolar. As características socioeconômicas não demostraram relação com consumo alimentar ou estado nutricional. Os valores de função pulmonar foram mais baixos em adolescentes e indivíduos com pior estado nutricional, porém sem diferença significante. Dados da metanálise, apesar da limitação amostral, apontaram o uso de probióticos como fator de proteção para exacerbações respiratórias, bem como para inflamação intestinal. Resultados da avaliação nutricional indicam que a transição das faixas etárias pré-escolar para escolar é um momento crítico, portanto abordagens direcionadas para estas faixas etárias podem ser de grande importância para preservação da saúde nutricional. Sendo assim, recomenda-se que mais estudos de estratégias nutricionais preventivas sejam realizados em faixas etárias precoces, como suplementação de probióticos, visando a melhora do prognóstico de pacientes com fibrose cística. / Cystic fibrosis is a hereditary disease characterized by deficiency of chloride transportation in epithelial cell membranes, resulting in thick and abnormal mucus, which may obstruct ducts of exocrine glands in several organs. The main clinical manifestations include the respiratory (recurrent and chronic lung infections) and gastrointestinal systems (pancreatic insufficiency and consequent maldigestion and absorption of nutrients, resulting in malnutrition). There is evidence that intestinal microbiota composition may impact the respiratory tract colonization of individuals with cystic fibrosis. This study aimed to verify current evidence regarding the effects of supplementation of probiotics, prebiotics or both in cystic fibrosis patients, concerning gastrointestinal and respiratory outcomes. We performed a systematic review and meta-analysis, and additionally carried out a survey of the nutritional status of patients with cystic fibrosis attending the outpatient clinic of the Instituto da Criança HCFMUSP. The systematic review and meta-analysis was performed according to the protocol proposed by the Cochrane Collaboration, searching electronic databases using the terms \"prebiotics\" or \"probiotics\" or \"symbiotic\", and \"cystic fibrosis\". Randomized clinical trials addressing intestinal inflammation and/or pulmonary exacerbations were included. The assessment of nutritional status was carried out through a cross-sectional survey of medical records concerning clinical and anthropometric data, and also by applying a questionnaire to patients and caregivers concerning food consumption, and socioeconomic characteristics. The bibliographic search identified 48 different studies, but only 6 fulfilled criteria to be included in the meta-analysis. A protective effect of probiotic and symbiotic use was observed in the rate of pulmonary exacerbations when compared to placebo (OR = -1.01 (95%CI -1.66, -0.37), p=0.002). The levels of fecal calprotectin (indicator of intestinal inflammation) had a significant reduction after intervention (OR = -12.18 (95%CI: -22.50, -1.86), p=0.02) and there was a decrease in the proportion of patients with intestinal inflammation (calprotectin> 50 mcg/g feces) with OR = 0.31 (95%CI: 0.13, 0.79), p=0.01. Regarding nutritional assessment, 101 patients were included (59.4% male, 86,4% white race), and median age at inclusion was 10 years old. The majority of patients were considered to be eutrophic and have adequate food intake, but lower values of BMI Z-score were observed in schoolchildren and adolescents. The proportion of underweight patients increased from 10% among preschoolers to 35% of the school age group. The socioeconomic characteristics were not associated to the food consumption or nutritional status. Lung function was lower in adolescents and individuals with poor nutritional status, but without significant difference. Data from the meta-analysis, despite the limitations of sample size, indicated that the use of probiotics may be a protective factor for respiratory exacerbations as well as intestinal inflammation. Results of the nutritional assessment indicate that the transition from the pre-school to the school age groups is a critical period, and therefore approaches directed to these age groups may have a significant impact in the nutritional health. Towards that, further studies using preventive nutritional strategies such as probiotic supplementation, are recommended for younger age groups, aiming to improve the prognosis of patients with cystic fibrosis.

INTRODUÇÃO: apesar da identificação de mais de 1500 mutações para o gene CFTR (cystic fibrosis transmembrane conductance regulator), o teste do suor ainda é o teste diagnóstico para Fibrose Cística (FC). O teste quantitativo de iontoforese por pilocarpina (TQIP) é o padrão-ouro para coleta do suor e análise do cloro, mas está sujeito a erros se não for realizado por técnicos qualificados. Embora a técnica de coleta do suor pelo sistema macroduct® e análise pela condutividade seja simples e tenha boa correlação com os níveis de cloro em estudos prévios, a mesma ainda é considerada como um teste de triagem para FC. O melhor ponto de corte para confirmar ou afastar a FC pelo método da condutividade deve ser ainda estabelecido. OBJETIVOS: comparar os valores de cloro no suor obtidos pelo teste quantitativo da iontoforese pela pilocarpina (teste clássico) com os valores de condutividade do suor obtido pelo sistema de coleta por macroduct® (teste simplificado) em pacientes com e sem FC e em uma amostra aleatória de pacientes em investigação para FC. O custo e o tempo despendidos na execução de cada teste foram também analisados na fase inicial do estudo. MÉTODOS: o teste do suor, pelas duas técnicas, foi realizado simultaneamente em pacientes com e sem FC e posteriormente em pacientes em investigação diagnóstica da doença no período de fevereiro/2006 a outubro/2008. Os pontos de corte para a condutividade para excluir ou diagnosticar FC foram < 75 e ? 90 mmol/L, respectivamente, e para o teste clássico cloro ? 60 e > 60 mmol/L. Na fase inicial da pesquisa (casos com e sem FC) foram utilizadas tabelas de contingência para os cálculos de sensibilidade (S), especificidade (E), valor preditivo positivo (VPP) e negativo (VPN), além do teste exato de Fisher para avaliar a associação entre os testes e a presença ou ausência de FC. Na amostra aleatória de pacientes usou-se a curva ROC também para os cálculos de S, E, VPP e VPN e também para calcular a área sob a curva entre os testes, e, em ambas as fases da pesquisa, para avaliar sua acurácia. Os respectivos intervalos de confiança de 95% (IC95%) também foram analisados. Para avaliação da concordância entre os testes, na amostra aleatória de pacientes, utilizou-se o coeficiente de kappa e o teste de McNemar. Aplicou-se o teste de Wilcoxon para se comparar os tempos na execução de cada teste, sendo considerados significativos quando p<0,05. RESULTADOS: 52 pacientes com FC (29M/23F; 1,5 a 18,2 anos) realizaram o teste do suor pelas duas técnicas, apresentando valores medianos de cloro e condutividade no suor de 114 e 122 mmol/L, respectivamente. A condutividade foi ? 95 mmol/L em todos os pacientes, conferindo ao teste 100% de sensibilidade (IC95%: 93,1 a 100%). Cinquenta pacientes sem FC (24M/26F; 0,5 a 12,5 anos) apresentaram valores medianos de cloro e condutividade no suor de 15,5 e 30 mmol/L, respectivamente. Em todos os casos a condutividade foi < 70 mmol/L, conferindo ao teste 100% de especificidade (IC95%: 92,9 a 100%). Foram então realizados 918 testes nos pacientes em investigação para FC, mas, em 180, as amostras foram inadequadas. Dos 738 testes realizados pelas duas técnicas, em 714 pacientes se afastou a FC, encontrando-se mediana de cloro de 11 mmol/L (variação: 3 a 137 mmol/L) e de condutividade de 25 mmol/L (variação: 14 a 138 mmol/L). Foram confirmados 24 pacientes com FC, encontrando-se uma mediana de cloro de 87 mmol/L (variação: 54 a 132 mmol/L) e de condutividade de 103 mmol/L (variação: 50 a 126 mmol/L). Pela curva ROC, com valores de condutividade > 90 mmol/L, obteve-se S= 83,3%, E= 99,7%, VPP= 90,9% e VPN= 99,4% para o diagnóstico de FC. Com valores de condutividade < 75 mmol/L praticamente se pôde excluir o diagnóstico de FC (VPN=99,7%; IC95%:99,0-100%). Houve excelente concordância entre o teste clássico e o simplificado, tanto pelo valor de kappa (0,934; IC95% 0,86 a 1,009), quanto pelo teste de McNemar (p=1,0000). O tempo despendido na execução dos testes foi significativamente menor com o teste simplificado (p<0,0001) e o custo do método simplificado foi discretamente inferior. CONCLUSÕES: o teste da condutividade do suor, seja em pacientes com diagnóstico previamente conhecido (com ou sem FC) ou quando realizado aleatoriamente, mostrou resultados superponíveis ao teste clássico e foi capaz de diferenciar pacientes com e sem FC. O teste simplificado apresentou alta sensibilidade e especificidade e houve excelente concordância entre os testes. O tempo de execução foi mais rápido e o custo inferior ao teste clássico. / INTRODUCTION: despite the identification of over 1500 CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations, the sweat test is still the diagnostic test for cystic fibrosis (CF). The quantitative pilocarpine iontophoresis test (QPIT) is the gold-standard method for collection of sweat and chloride analyses, but is subjected to errors if not performed by qualified technicians. Although the technique using the macroduct system for sweat collection and the conductivity analysis is simpler and has good correlation with chloride levels in previous studies, it is still considered a screening test for CF. The best cut-off point of sweat conductivity to confirm or rule out CF must yet be established. OBJECTIVES: to compare the sweat chloride values obtained by the quantitative pilocarpine iontophoresis test (classic test) with sweat conductivity analysis obtained by the macroduct (simplified test) in patients with a confirmed CF diagnosis, in patients without CF and in a random sample of patients being investigated for CF. The cost and time spent to perform each test were also analysed in the initial phase of the study. METHODS: both techniques of sweat test were simultaneously performed initially in patients with CF, afterwards in patients in whom CF had been ruled out and finally in patients referred for a sweat test between February 2006 and October 2008. The cut-off values for sweat conductivity to exclude or diagnose CF were = 90 mmol/L and for the QPIT were sweat chloride ? 60 e > 60 mmol/L, respectively. Contingency tables were used in the initial phase of the study (cases with or without CF) for calculation of sensitivity (Se), specificity (Sp), positive (PPV) and negative predictive value (NPV) and Fisher\'s exact test was used to assess the association between the tests and the presence or absence of CF. ROC curve was used in the random sample of patients also for calculation of Se, Sp, PPV and NPV and also to calculate the area under the curve between both tests in both phases of the study to assess their accuracy. The respective 95% confidence intervals (95%CI) were also analysed. Kappa coefficient and McNemar tests were used for evaluation of agreement between the tests in the random sample of patients. Wilcoxon test was used to compare the time spent to perform each test, with the significant difference set at p < 0.05. RESULTS: in 52 CF patients (29M/23F, age range 1.5 to 18.2y) the median value of sweat Cl and conductivity were 114 and 122 mmol/L, respectively. All patients had sweat conductivity values above 95 mmol/L (100% sensitivity; 95%CI: 93.1 to 100%). In 50 patients without CF (24M/26F, age range 6m to 12.5y) the median value of sweat Cl and conductivity were 15.5 and 30 mmol/L, respectively. All patients had conductivity values bellow 70 mmol/L (100% specificity; 95%CI: 92.9 to 100%). Nine hundred and eighteen tests were then performed in patients being investigated for CF but 180 had inadequate samples. Of the 738 tests performed with both techniques in 714 CF was ruled out, with median values of sweat Cl of 11 mmol/L (range: 3 to 137 mmol/L) and of conductivity of 25 mmol/L (range: 14 to 138 mmol/L). Twenty four patients had a diagnosis of CF presenting a median sweat Cl of 87 mmol/L (range: 54 to 132 mmol/L) and a median conductivity value of 103 mmol/L (range: 50 to 126 mmol/L). The ROC curve showed that with a conductivity value > 90 mmol/L sensitivity of 83.3%, specificity of 99.7%, PPV of 90.9% and NPV of 99.4% was obtained to diagnose CF. The best conductivity cut-off value to exclude CF was < 75 mmol/L (NPV=99.7%; IC95%:99.0-100%). Good agreement were observed between the tests (kappa: 0.934; IC95% 0.86 a 1.009; McNemar test: p=1.0000). The time spent to perform the tests was significantly lower with the simplified test (p<0.0001) and the cost was slightly lower with the conductivity test. CONCLUSIONS: sweat conductivity performed in patients with a known CF or non-CF diagnosis or randomly applied in subjects referred for a sweat test showed similar results as the classic test and could differentiate patients with or without CF. Conductivity test had a high sensitivity and specificity and good agreement was observed between the techniques. The time spent to perform the tests was lower with the simplified test, as well as the cost.

La persistance bactérienne implique une adaptation aux conditions et aux contraintes environnementales, parfois associée à une diversification des génotypes et des phénotypes des populations bactériennes impliquées. Dans le cadre des infections chroniques, la mucoviscidose (CF) est une des pathologies humaines parmi les plus étudiées en termes de persistance et d’adaptation de pathogènes opportunistes. Certains pathogènes opportunistes d’origine environnementale, comme les bactéries des genres Achromobacter et Pandoraea, considérés comme émergents dans cette pathologie, sont capables de coloniser chroniquement les voies respiratoires des patients CF (VRCF). La colonisation et la persistance impliquent des mécanismes d’adaptations étudiés pour P. aeruginosa mais mal connus pour les bactéries émergentes.Nous avons étudié la persistance de bactéries du genre Achromobacter dans les VRCF de 13 patients, ainsi que dans de réseau d’eau d’un centre de soins dentaires, et la persistance de Pandoraea pulmonicola dans les VRCF d’un patient, durant des périodes de colonisation allant jusqu’à 7 ans. En parallèle, nous avons étudié la diversité génomique et phénotypique de populations d’Achromobacter dans les expectorations de 9 patients. Enfin, une investigation environnementale au domicile de 3 patients colonisés chroniquement par Achromobacter a été menée dans le but de connaître la diversité et l’écologie des bactéries de ce genre dans l’environnement proche des patients. Lors de ces différentes études, les espèces d’Achromobacter et Pandoraea ont été identifiées par méthodes moléculaires et la dynamique du génome ainsi que la diversité phénotypique ont été étudiées.Nous avons observé une diversité d’espèces de bactéries du genre Achromobacter colonisant les VRCF, incluant une espèce non décrite. Les patients colonisés chroniquement l’étaient par un clone unique d’Achromobacter ou de P. pulmonicola, appuyant l’idée de l’acquisition initiale d’un clone environnemental qui persiste dans le temps. Une importante diversité génomique et phénotypique a été observée au cours du temps mais aussi au sein de populations à un temps donné. Nous avons également mis en évidence une importante diversité de profils d’antibiorésistance au sein de chaque expectoration, dont l’impact clinique reste à évaluer. Enfin, une diversité d’espèces du genre Achromobacter a été observée au domicile des patients alors que le clone d’A. xylosoxidans adapté aux VRCF des patients n’a pas été isolé dans leurs environnements domestiques. Ces résultats suggèrent qu’après la colonisation initiale et la spécialisation des clones colonisant les VRCF, ceux-ci seraient secondairement incapables de survivre dans l’environnement.Un clone qui colonise les VRCF s’adapte rapidement aux conditions environnementales particulières de cet habitat et subit une diversification génomique et phénotypique intense par spécialisation de génotypes à différentes niches écologiques, aboutissant à une population clonale diversifiée. Cette diversité assure certainement la persistance de la population clonale par "l’hypothèse d’assurance" selon laquelle quelle que soit la pression environnementale exercée, une bactérie ou un sous-groupe de bactéries sera capable d’y résister.Mots clés : Achromobacter, adaptation, colonisation chronique, diversité, écologie, environnement, épidémiologie, évolution, génomique, mucoviscidose, Pandoraea, persistance, phénotype, réseau d’eau, résistance aux antibiotiques. / Bacterial persistence involves adaptation to environmental conditions and constraints, sometimes associated with genotype and phenotype diversification of bacterial populations. In the context of chronic infections, Cystic Fibrosis (CF) is a human disease among the most studied in terms of persistence and adaptation of opportunistic pathogens. Some environmental opportunistic pathogens like Achromobacter and Pandoraea genera are considered as emerging in CF and are able to chronically colonize CF Respiratory Tract (CFRT). Adaptation mechanisms required for colonization and persistence were studied for P. aeruginosa but remain largely unknown for emerging bacteria. We studied Achromobacter spp. persistence in the CFRT of 13 patients and in a dental care unit water network, and Pandoraea pulmonicola persistence in the CFRT of one patient, during colonization periods up to 7 years. In parallel, we studied Achromobacter population genomic and phenotypic diversity in sputum samples from 9 patients. Finally, we made an environmental investigation to study the diversity and the ecology of Achromobacter spp. in household of 3 Achromobacter chronically colonized CF patients. During these studies, Achromobacter and Pandoraea species were identified by molecular methods and genome dynamic and phenotypic diversity were studied.Diversity of Achromobacter species colonizing the CFRT is described and included an undescribed species. Chronically colonized patients had a unique Achromobacter or Pandoraea clone in their CFRT, supporting the initial acquisition of one environmental clone which persists over time. A large genomic and phenotypic diversity has been observed over time and also at the intra-specimen level. A wide antibiotic susceptibility profile diversity was observed within samples and its clinical impact remains to be assessed. Finally, Achromobacter species diversity was observed in patient domestic environment but the Achromobacter clone adapted to the patient CFRT was not isolated. These results suggested that after initial colonization and specialisation the CFRT, colonizing clones might secondarily be unable to survive in the environment.A colonizing clone quickly adapts to the specific local conditions of the CFRT and undergoes intense genomic and phenotypic diversification with genotype specialization to the different ecological niches of the heterogeneous CFRT, resulting in a diversified clonal population. This diversity certainly insures the population persistence according to the “bet hedging” theory stating that regardless of the environmental pressures, a bacteria or a subgroup of bacteria will be able to persist.Key words : Achromobacter, adaptation, antibiotic susceptibility, chronic colonization, Cystic Fibrosis, diversity, ecology, environment, epidemiology, evolution, genomic, Pandoraea, persistence, phenotype, water network.