Le développement d’une nouvelle sonde dite « activity-based probe » pour réaliser la détection de formes actives de protéases appartenant à la famille des protéases à zinc de la matrice (MMP) a été réalisé dans ce travail, en partant d’un inhibiteur phosphinique puissant des MMP dans lequel a été introduit un groupement photoactivable de type diazérine. Ce composé se révèle un inhibiteur puissant de plusieurs MMP avec des affinités nanomolaires. Ce composé incubé avec différentes MMP est par ailleurs capables de modifier de façon covalente un grand nombre de MMP au niveau de leur site actif, avec des rendements de modification variant de plus de 50% à 11%, selon la nature des MMP. En ayant choisi comme moyen de détection la radioactivité, nous démontrons qu’avec cette nouvelle sonde qu’il est possible de détecter des formes actives de MMP avec des sensibilités de l’ordre de la femtomole dans des systèmes modèles de protéomes complexes. Appliquée à l’analyse de lavages broncho alvéolaires de souris traitées par voie pulmonaire avec des nanoparticules pour induire une réponse inflammatoire, cette nouvelle sonde permet de mettre en évidence la présence de formes actives du domaine catalytique de la MMP-12, une métalloprotéase à zinc exprimée par les macrophages, mais pas dans les animaux contrôles. En revanche l’analyse de carotides humaines de patients souffrant d’athérosclérose ne nous pas conduit avec cette sonde à la détection de formes actives de MMP. Malgré ce résultat, il est à noter que la détection de forme active de MMP dans un fluide pathologique est une première dans ce domaine. Cette sonde étant validée pour sa capacité à détecter des formes actives de MMP, elle permettra dans l’avenir de tester d’autres fluides pathologiques d’origine humaine ou bien des extraits de tissu comme des tumeurs pour lesquels les MMP pourraient être des marqueurs de ces pathologies. / A new activity-based probe able to covalently modify the active site of proteases belonging to the matrix metalloprotease family (MMPs) has been developed in this thesis project. The probe was shown to behave as potent inhibitor of several MMPs, with nanomolar Ki values. This probe was also able to modify specifically only the free active site of MMPs, with particular high yields of cross-linking varying from 50 % to 11 %, depending of the MMPs tested. Using radioactivity as means of detection, this probe was able to detect active form of MMPs with a threshold of 1 femtomole. Applied to the study of bronchoalvelolar fluids (BAL) from mice exposed to nanoparticles by a lung aspiration protocol, this probe revealed the presence of the catalytic domain of MMP-12 under its active form, but not in control animals. When used to detect active form of MMPs from extracts obtained from human arteries of patient suffering from atherosclerosis, the probe was not able to detect such MMP active forms. Despite this negative result, the detection of active form of MMP in pathological fluid like BAL has never been reported before this work. Having validated this novel MMP activity-based probe, it will be possible to use it now for detecting MMPs from other pathological fluids or tissues extracts in which MMPs can be good markers of the pathology.

Abstract Pulmonary fibrosis, lung cancer and chronic obstructive pulmonary disease (COPD) are severe diseases and common death causes worldwide. Due to the lack of an effective therapy, the investigation of cell biological mechanisms behind these diseases is essential. An activation of stromal cells, including myofibroblasts, is a main feature found in the pathogenesis of lung diseases. Myofibroblasts express alpha-smooth muscle actin (α-SMA), have specific ultrastructure, produce extracellular matrix proteins and possess contractile capacity. Detailed structure and function of myofibroblasts and their roles in healthy and diseased lung are not yet wholly understood. The investigation of the myofibroblasts may further offer novel tools for the acquisition of proper diagnosis, prognosis and medical treatment. The study aimed to characterize the ultrastructural, functional and disease-specific features of stromal cells, particularly myofibroblasts, in interstitial and malignant lung diseases. The functional properties evaluated here were differentiation, invasive and contractile properties. The study material included in vitro stromal cells cultured from bronchoalveolar lavage (BAL) fluids. The appearance and location of myofibroblasts in different lung compartments of non-smokers and the COPD-patients were examined in vivo. The cells were investigated by light and electron microscopy. The α-SMA expression was analysed by gene or protein assays. The study demonstrated that stromal cells could be cultured from diagnostic BAL fluid samples and lung tissues. Cultured cells were a mixture of fibroblasts and myofibroblasts. A small proportion of cells exhibited progenitor-like features. Myofibroblasts revealed differential features in electron microscopy and invasive or contractile assays. When studying tissues from healthy and COPD lungs, myofibroblasts were located both in alveoli and airways. In alveoli myofibroblasts localized in widened alveolar tips which were newly described structures and locations of myofibroblasts in healthy and diseased lung. The amount of myofibroblasts in large airways, but not in peripheral lung, was increased in COPD. We concluded that myofibroblasts have several locations in normal and COPD lung, which suggests a function both in pulmonary regeneration and the pathogenesis of COPD. Smoking altered the phenotype of myofibroblasts regardless of its origin. / Tiivistelmä Keuhkofibroosi, keuhkosyöpä ja keuhkoahtaumatauti (COPD) ovat kansallisesti ja maailmanlaajuisesti yleisiä ja kuolemaan johtavia sairauksia. Taudinmääritys ja hoito ovat vaativia, eikä kaikille potilaille ole parantavaa hoitoa. Keuhkosairauksien kaikkia solubiologisia mekanismeja ei vielä tunneta, mikä on yksi syy lääkekehityksen ongelmiin. Interstitiaaleissa ja pahanlaatuisissa keuhkosairauksissa esiintyy paljon aktiivisia sidekudossoluja, kuten muuntuneita fibroblasteja eli myofibroblasteja. Ne tunnistetaan hienorakenteesta, jota voidaan tutkia elektronimikroskoopilla. Myofibroblastit ilmentävät myös solun sisäistä sileän lihaksen alfa-aktiinia (α-SMA), tuottavat sidekudoksen proteiineja ja kykenevät supistumaan. Myofibroblastien hienorakenteen ja toiminnan selvittäminen voi antaa lisätietoa keuhkosairauksien syntymekanismeista, jolloin diagnostiikkaa, ennustetta sekä hoitoja voidaan arvioida paremmin. Väitöskirjassa selvitettiin myofibroblastien hienorakennetta ja toimintaa eri keuhkosairauksissa. Tutkitut toiminnalliset ominaisuudet olivat erilaistumispotentiaali, invasiivisuus ja supistumiskyky. Sairauksien kliinistä käyttäytymistä ja potilaiden tupakointitottumuksia tarkasteltiin suhteessa solubiologiatason havaintoihin. Tutkimusmateriaali kerättiin taudinmäärityksen yhteydessä interstitiaalisia keuhkosairauksia, keuhkoahtaumatautia tai keuhkosyöpää sairastavilta potilailta. Tulosten mukaan bronkoalveolaarihuuhtelunesteestä (BAL) ja keuhkokudospaloista voidaan soluviljelymenetelmin kasvattaa ja ylläpitää solulinjoja. Viljellyt solut muodostivat sekasolupopulaatiota, joissa esiintyi pääosin fibroblasteja ja vaihteleva osuus myofibroblasteja. Pieni osa soluista ilmensi kantasoluille tyypillisiä piirteitä. Myofibroblastien tyyppipiirteet ja toiminnalliset ominaisuudet vaihtelivat taudeittain. Kudoksessa myofibroblasteja ilmentyi sekä keuhkorakkuloissa että ilmateissä. Keuhkorakkulatasolla myofibroblastit sijoittuivat irrallisten alveoliseinämien laajentuneisiin päihin, joita ei ole aiemmin tutkittu tieteellisessä kirjallisuudessa myofibroblastien yhteydessä. Keuhkoahtaumatauti ja tupakointi vähensivät näiden rakenteiden määrää perifeerisessä keuhkossa, kun taas suurissa ilmateissä keuhkoahtaumatauti lisäsi myofibroblasteja. Päättelimme, että myofibroblastit edistävät keuhkoahtaumataudin syntyä isoissa ilmateissä, mutta saattavat osallistua keuhkojen korjaukseen keuhkorakkuloissa ja pienissä ilmateissä.

Die Frage nach adäquaten mikrobiologischen und molekulargenetischen Methoden, um die Kolonisation des Respirationstrakts von Mukoviszidose-Patienten mit Pseudomonas aeruginosa nachzuweisen und zu charakterisieren, wird kontrovers diskutiert. Von 38 klinisch stabilen Patienten mit cystischer Fibrose (CF) wurden sequentiell im Abstand von 18 Monaten Proben aus Rachenabstrich, Sputum und Bronchiallavage (BAL) entnommen und bezüglich Pseudomonas-Nachweis untersucht. Die Pseudomonas-Stämme wurden mittels Random Amplified Polymorphic DNA (RAPD)-Analyse und Pulsfeld-Gelelektrophorese (PFGE) von DNA-Makrorestriktionsfragmenten typisiert und bezüglich der Frage nach genetisch divergierenden Isolaten innerhalb des selben Individuums sowie nach möglichen longitudinalen genetischen Veränderungen evaluiert. Sensitivität, negative und positive prädiktive Werte und Spezifität, um eine P. aeruginosa-Besiedlung zu erkennen, waren 36%, 74%, 83% und 96% im Falle der Kulturen aus dem Oropharynx von nicht-expektorierenden Patienten und 92%, 94%, 100% und 100% für Sputumkulturen von expektorierenden Probanden. RAPD-Analyse und PFGE waren in der Lage, zwischen unterschiedlichen Pseudomonas-Stämmen zu diskriminieren, wobei nur die DNA-Makrorestriktion zwischen Subtypen unterscheiden konnte. Die Genotypen der Pseudomonas-Isolate aus Rachenabstrich und Sputum divergierten in 55% und 40% zu den Isolaten der BAL. Longitudinale Variationen des Genotyps wurden in 62% der Fälle beobachtet, die Hälfte davon war nur mittels bronchoskopisch gewonnener Proben erkennbar. Zusammengefasst besitzen Sputumproben bezüglich des Pseudomonas-Nachweises dieselbe Wertigkeit wie Kulturen aus der BAL, während Rachenabstriche in einer frühen Krankheitsphase für die Charakterisierung der bakteriellen Flora des unteren Respirationstrakts wenig geeignet sind. Die Methode der DNA-Makrorestriktion kann als zuverlässige Technik für epidemiologische Untersuchungen empfohlen werden. Unterschiedliche Genotypen innerhalb desselben Individuums und longitudinale genetische Alterationen sind häufig, jedoch unter Umständen nur bronchoskopisch nachweisbar. / There is controversy about adequate specimen to detect and characterise colonisation of cystic fibrosis (CF) airways by Pseudomonas aeruginosa. Oropharyngeal, sputum and bronchoalveolar lavage (BAL) samples were evaluated sequentially from 38 stable CF patients for the detection of P. aeruginosa. Pseudomonas strains were typed by random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. The occurrence of genetically different isolates within the same host and longitudinal variations in the genotype during repeated examinations was assessed. Sensitivity, negative and positive predictive values and specificity to detect P. aeruginosa were 36%, 74%, 83% and 96% for oropharyngeal cultures in non-expectorating patients and 92%, 94%, 100% and 100% for sputum cultures from expectorating patients, respectively. RAPD analysis and PFGE were suitable to characterize P. aeruginosa CF isolates, although only DNA macrorestriction was able to distinguish between identical and closely related strains. Genotypes of Pseudomonas isolates recovered from oropharyngeal swabs and sputum differed to the strains recovered by bronchoscopy in 55% and 40%, respectively. In 62% longitudinal variations in the genotype occurred. Half of these alterations were only detectable from bronchoscopically obtained samples. In conclusion, sputum samples have the same value as specimens from BAL to detect P. aeruginosa colonisation, whereas cultures from the oropharynx are not suitable for characterising the bacterial conditions in the CF lungs in an early disease state. DNA macrorestriction is recommended as an excellent tool for epidemiological investigations. Different genotypes within the same host and longitudinal genetic alterations are common and may be detectable in the BAL fluid exclusively.

Doctor of Philosophy (PhD) / Asthma is a chronic inflammatory disease of the airways. Corticosteroid medication is the most effective currently available treatment. Complications of corticosteroid therapy are dose-dependent, however, the clinical efficacy of varying doses of inhaled corticosteroids has been studied with mixed results. A randomized, double-blind, parallel group study was used to evaluate the inhaled corticosteroid dose-response relationship for clinical endpoints and in vitro parameters of underlying airway inflammation and remodelling. The mannitol provocation test with Forced Oscillation Technique (FOT) was used to derive potential dose-differentiating endpoints. In vitro inflammatory markers were measured in alveolar macrophages from bronchoalveolar lavage. Basement membrane thickness was measured from bronchial biopsies. Eleven nonasthmatic subjects were enrolled for comparison. This thesis addresses the null hypothesis that there is no significant difference in clinical and biological effects between low dose (200mcg/day, n=11) and high dose (1000mcg/day, n=11) treatment (for 6-7 weeks) with inhaled fluticasone propionate (FP) for a range of clinical outcomes and in vitro markers of airway inflammation and remodelling. Significant changes after FP included increased FEV1, reduced airway hyperresponsiveness (AHR) (by FOT and FEV1), exhaled nitric oxide and Juniper symptom score. In addition, significant reductions occurred in expression of GM-CSF, TNF-alpha and IL-1ra in macrophages. A lower baseline FOT-derived respiratory system conductance was predictive of a greater degree of improvement in symptoms. No statistically significant differences in the changes after treatment between low and high dose FP were found in spirometry, exhaled nitric oxide, symptom scores, AHR, alveolar macrophage cytokine levels (GM-CSF, TNF-alpha, IL-1ra, IL-10) and basement membrane thickness, although there were trends towards greater improvements in many of the parameters after high dose FP. Basement membrane thickness appeared to be reduced by high dose FP, although this reduction was not statistically significant. There was a weak, but statistically significant, negative correlation between basement membrane thickness and FOT-derived conductance (r2=0.135, p=0.042). With the recognition of the limitations in the interpretation of these data, the results suggest that, in previously steroid naïve mild to moderate asthmatics, there may be only minimal benefit derived from an additional 800µg/day of inhaled fluticasone above the low dose of 200µg/day.