La mucoviscidose (CF) est la maladie génétique récessive létale la plus fréquente dans la population caucasienne. Elle est caractérisée par une obstruction et des infections des voies respiratoires et une inflammation chronique. La morbidité et la mortalité sont principalement dues à l'atteinte pulmonaire, qui est variable chez les patients, même lorsqu’ils sont porteurs du même génotype. Les facteurs responsables sont multiples : les mutations dans CFTR (le gène responsable de la maladie), les gènes modificateurs, mais aussi les facteurs environnementaux et les modifications épigénétiques. L'objectif principal de ce projet était de déterminer s'il y avait une corrélation entre la méthylation de l'ADN et la sévérité de l'atteinte pulmonaire chez les patients CF. Nous avons obtenu la cohorte METHYLCF (49 patients CF p.Phe508del homozygotes et 24 témoins sains) ainsi qu’une biobanque d'ADN à partir de sang total et de cellules épithéliales nasales (NEC). Les patients CF ont été stratifiés en fonction de leur VEMS, ajusté à l’âge. D’une part, nous avons analysé la méthylation de l'ADN dans CFTR plus 13 gènes modificateurs en utilisant la méthode de conversion au bisulfite et séquençage de nouvelle génération (plateforme 454 Roche). D’autre part, nous avons réalisé une analyse pan-génomique de la méthylation de l'ADN avec la plateforme 450k BeadChip (Illumina). Les sites différentiellement méthylés (DMS) sélectionnés ont été validés par pyroséquençage (PyroMark Q24, Qiagen). Deux gènes modificateurs ont été identifiés comme différentiellement méthylés chez les patients CF par rapport aux témoins: EDNRA dans le sang et HMOX1 dans le sang et dans les NEC. De façon intéressante, dans les NEC, la méthylation de EDNRA, HMOX1 et GSTM3 a été corrélée avec la sévérité de l’atteinte pulmonaire. De plus, de faibles niveaux de méthylation d'ADN dans GSTM3 ont été associés à la présence de l'allèle GSTM3*B, un polymorphisme de séquence qui a un effet protecteur chez les patients CF. Grâce à l'analyse tout-génome, nous avons identifié 1267 DMS, associés à 638 gènes, chez les patients CF par rapport aux témoins, et 187 DMS, associés à 116 gènes, chez les patients CF sévères par rapport aux modérés. Parmi ces gènes, il y a de nombreux gènes importants pour l’adhésion cellulaire et les réponses immunitaire et inflammatoire. Les DMS identifiés sont enrichis dans des régions prédites comme enhancers, pouvant représenter des séquences régulatrices, mais également en régions intergéniques. De façon intéressante, 80 gènes différentiellement méthylés sur 638 étaient différentiellement exprimés (méta-analyse de données transcriptomiques disponibles). Six sur neuf DMS sélectionnés ont été validés et cinq DMS sur six ont été répliqués dans une population indépendante. De plus, 23 DMS, dont 10 intergéniques, étaient corrélés avec le VEMS. Notre étude a montré que la méthylation de l'ADN est profondément modifiée dans le sang et dans les NEC des patients CF. Des faibles changements de méthylation de l'ADN ont été observés dans des gènes modificateurs connus ; des changements de méthylation plus importants ont été observés dans d'autres gènes qui pourraient représenter de nouveaux modificateurs de la fonction pulmonaire. Ensemble, ces gènes pourraient moduler la sévérité de l’atteinte pulmonaire chez les patients CF. / Cystic fibrosis (CF) is the most common life-threatening recessive genetic disease in the Caucasian population. It is characterized by airway obstruction, respiratory infection and inflammation. Morbidity and mortality are mainly due to lung disease, which is variable among CF patients, even for those having the same genotype. Contributing factors are mutations in CFTR (the disease-causing gene), modifier genes, but also environmental factors and epigenetics. The main goal of this project was to determine whether there was a correlation between DNA methylation and the severity of CF lung disease. We built the METHYLCF cohort (49 p.Phe508del homozygous CF patients and 24 healthy controls) and a DNA biobank from whole blood and nasal epithelial cells (NEC). CF patients were stratified accordion to their FEV1% predicted, adjusted to age. We profiled DNA methylation at 14 modifier genes using bisulfite conversion and next-generation sequencing (454 Roche). Genome-wide DNA methylation was analyzed with the 450K Beadchip (Illumina). Selected differentially methylated sites (DMS) were validated by pyrosequencing. Using the candidate modifier gene approach, we showed that two CF modifier genes were differentially methylated in CF patients compared to controls: EDNRA in blood and HMOX1 in blood and NEC. Methylation of EDNRA, HMOX1 and GSTM3 was associated with lung disease severity in NEC. Interestingly, low DNA methylation levels at GSTM3 were associated with the GSTM3*B allele, a polymorphic 3-bp deletion that has a protective effect on CF patients. In addition, through the genome-wide analysis, we identified 1267 DMS, associated with 638 genes, between CF patients and controls and 187 DMS, associated with 116 genes, between severe CF and mild CF patients. DMS were enriched at predicted enhancers, which may represent regulatory sequences, and also at intergenic regions. Gene ontology analyses highlighted cellular processes relevant to CF, i.e. cell adhesion and inflammatory and immune response. Interestingly, 80 out of 638 differentially methylated genes were differentially expressed in publicly available NEC transcriptomic data. Six out of 9 selected DMS were validated and five out of six DMS were replicated in an independent set of patients. Additionally, 23 DMS, 10 of which were intergenic, correlated with FEV1% predicted. Our study has shown that DNA methylation is altered in blood and NEC of CF patients. Small DNA methylation changes were observed at known CF modifier genes; more dramatic DNA methylation changes were found at other genes that may impact lung function. Collectively, these epigenomic variations may lead to different degrees of lung disease severity in CF patients.

70% des mutations identifiées sur le gène responsable de la mucoviscidose correspondent à la délétion de la phénylalanine en position 508 (F508del) de la protéine CFTR (Cystic Fibrosis Transmembrane conductance Regulator). Cette mutation est responsable, à 37°C, d'un mauvais repliement, du blocage et de la dégradation rapide de CFTR au niveau du réticulum endoplasmique (RE), et par conséquent de l'absence de sécrétion des ions Cl- au niveau de la membrane apicale des cellules épithéliales. Deux conséquences principales de cette mutation sont un épaississement important du mucus bronchique et une diminution de l'intégrité de la barrière luminale de l'épithélium bronchique. Ces deux phénomènes participent à l'invasion et à l'infection du tissu pulmonaire par des bactéries pathogènes comme Pseudomonas aeruginosa, exacerbant l'inflammation et la destruction tissulaire au niveau des poumons. L'objectif de cette étude a été de déterminer le rôle de deux protéines appartenant à la famille des protéines G hétérotrimériques, G12 et G13, dans la dégradation de la protéine CFTR-F508del ainsi que dans le contrôle des complexes jonctionnels au niveau de l'épithélium bronchique sain et mucoviscidosique. Nos travaux démontrent pour la première fois que dans la mucoviscidose, l'expression des protéines G12 et G13 est faible. Nous avons aussi montré que G12, et non G13, est impliquée dans le contrôle de la dégradation de la protéine CFTR-F508del via les protéines chaperonnes Calnexine et HSP90, et dans la formation et le maintien des jonctions cellulaires bronchiques via E-cadhérine et ZO-1 de manière inverse par rapport à l'épithélium rénale. Ces travaux placent donc G12 comme un acteur non négligeable de la maladie de la mucoviscidose. / F508del, the most frequent mutation found in cystic fibrosis (CF) population, impacts CFTR (Cystic Fibrosis Transmembrane conductance Regulator) trafficking and causes its rapid degradation at the endoplasmic compartment, resulting in a significant decrease in Cl- secretion at the apical membrane of epithelial cells. F508del has two main features, significant thickening of the bronchial mucus and a reduction in the integrity of the luminal barrier of the bronchial epithelium. These two phenomena are involved in the invasion and infection of lung tissue by pathogenic bacteria such as Pseudomonas aeruginosa, exacerbating the inflammation and lung destruction. The objective of this study was to determine the role of two proteins member of the heterotrimeric G proteins family, G12 and G13, in the degradation of the F508del CFTR, and in the control of junctional complexes in the normal and CF bronchial epithelium. Our results show for the first time that G12 and G13 are down expressed in CF. G12, but not G13, is involved in the control of F508del-CFTR degradation through its interaction with Calnexin and HSP90 chaperones. Unlike kidney epithelia cells, G12 promotes the formation and maintenance of cell junctions in the bronchial epithelium by affecting E-cadherine and ZO-1 stability. Altogether, our results set therefore G12 as a significant actor of the CF disease.

Cystic fibrosis (CF) is genetically conditioned, autosomal recessive disease that occurs in the European population with a prevalence of about 1:2500 - 1:1800. In this disease we observe a mutation of the CTFR gene with subsequent fault in chloride channels. Such afflicted individuals usually suffer from chronic respiratory problems, pancreatic insufficiency, high concentration of chloride ions in sweat and obstructive azoospermia. Genetic testing of CFTR gene is indicated in individuals who meet the CF clinical picture and a positive sweat test (increased concentration of chlorides in the sweat). Genetic testing of the CFTR gene is usually done by using commercial kits detecting the most common mutations of the CFTR gene in the Czech Republic. If the testing results are negative, it is further performed an MLPA method that captures the larger deletions and duplications of gene, eventually a sequencing of all exons is. Despite the well-established algorithm of the testing, some patients suffering from symptoms of CF are left without genetic findings. Thanks to development of next generation sequencing, it is possible to make the diagnosis of CF more effective and uncover the variants that were not captured by previous methods.

[pt] A fibrose cística é uma doença genética causada por mutações no gene CFTR, que implica na alteração do transporte de íons pela membrana das células de diversos órgãos, aumentando a quantidade e viscosidade do muco, suor e secreções pancreáticas. A principal consequência são os danos pulmonares, caracterizados por frequentes infecções e insuficiência respiratória. Com isso, vários estudos vêm sendo desenvolvidos ao longo dos anos, com o intuito de descobrir fármacos que possam agir como moduladores do CFTR, melhorando a função pulmonar desses pacientes. O presente trabalho teve o objetivo de sintetizar derivados de 3-fenilindeno[1,2-d][1,2,3]triazol-8(3H)-ona, 3-fenil-3,4- di-hidro-9H-[1,2,3]triazolo[4,5-b]quinolin-9-ona e 3-(1-fenil-1H-1,2,3-triazole-4- carbonil)quinolin-4(1H)-ona caracterizar a relação estrutura atividade desses compostos como potenciadores do CFTR. Para a síntese de 3-fenilindeno[1,2-d][1,2,3]triazol-8(3H)-ona inicialmente utilizou-se a 2 bromoacetofenona para, através do reagente de Gold produzido a partir do cloreto de cianurila, produzir a enaminona. A etapa chave de obtenção dos triazóis foi realizada através de uma reação de cicloadição entre as (E)-3-(dimetilamino)-1-(2-nitrofenil)prop-2-en-1-ona e aril azidas azido-benzeno, 1-azido-4-bromo-benzeno, 1-azido-4- nitrobenzeno e ácido 4-azido-benzóico. Foram obtidos quatro compostos com rendimentos entre 20 por cento e 50 por cento. Foram realizadas tentativas de ciclização intramolecular catalisada por paládio na presença de fosfinas, porém o produto esperado não foi obtido. Para a obtenção da 3-fenil-3,4-di-hidro-9H-[1,2,3]triazolo[4,5-b]quinolin-9-ona obteve-se o intermediário (E)-3-(dimetilamino)-1-(2-nitrofenil)prop-2-en-1-ona, que através de uma reação de cicloadição com a azido-benzeno obteve-se o triazol com rendimento de 30 por cento. A proposta seria a redução do grupo nitro para amina, e posterior substituição da amina por azida, para fazer a arilação intramolecular do triazol via catálise fotoredox. Para a obtenção de 3-(1-fenil-1H-1,2,3-triazole-4-carbonil)quinolin4(1H)-ona foram utilizados anilina e dietil etoximetilenomalonato como precursores para sintetizar 4-oxo-1,4-di-hidroquinolino-3-carboxilato de etilo, que foi obtida com rendimento de 50 por cento. Realizou-se uma reação de adição de alcino seguida da eliminação de etanol, para obter a 3-(1-fenil-1H-1,2,3-triazole-4-carbonil)quinolin-4(1H)-ona com etiniltrimetilsilano e então realizar uma reação click com azidas. Todos os compostos obtidos foram caracterizados por RMN1H e RMN13C. / [en] Cystic fibrosis is a genetic disease caused by mutations in the CFTR gene, which involves changing the transport of ions across the membrane of various organ cells, increasing the amount and viscosity of the mucus, sweat and pancreatic secretions. The main consequence is lung damage, characterized by frequent infections and respiratory failure. Several studies have been developed over the years with the intention of discovering drugs that can act as modulators of CFTR, improving the lung function of these patients. The present work aimed to synthesize derivatives of 3-phenylindeno[1,2-d [1,2,3]triazol-8(3H)-one, 3-phenyl-3,4-dihydro-9H-[1,2,3]triazolo[4,5-b]quinolin-9-one and 3-(1-phenyl-1H1,2,3-triazole-4-carbonyl)quinolin-4(1H)-one to characterize the relationship structure of these compounds as enhancers of CFRT. For the synthesis of 3-phenylindeno[1,2-d][1,2,3]triazol-8(3H)-one, the 2-bromoacetophenone was initially used to produce the (E)-3-(dimethylamino) -1- (2-nitrophenyl) prop-2-en1-one through the Gold reagent obtained from the cyanuric chloride. The key step of obtaining the triazoles was accomplished by a cycloaddition reaction between the (E)-3-(dimethylamino)-1-(2-nitrophenyl) prop-2-en-1-one and the aryl azides azido-benzene, 1-azido-4-bromo-benzene, 1-azido-4-nitrobenzene and 4-azido benzoic acid. Four compounds in yields between 20 percent and 50 percent were obtained. Attempts were made for intramolecular cyclization catalyzed by palladium in the presence of phosphines, but the expected product was not obtained. To obtain 3- phenyl-3,4-dihydro-9H-[1,2,3]triazolo[4,5-b]quinolin-9-one, first It was obtained the intermediate (E)-3- (dimethylamino)-1-(2-nitrophenyl) prop-2-en-1-one through cycloaddition reaction with the azido-benzene gave the triazole in 30 percent yield. The proposal would be the reduction of the nitro group to amine, and subsequent replacement of the amine with azide, to make the intramolecular arylation of triazole via photoredox catalysis. To obtain 3-(1-phenyl-1H-1,2,3-triazole-4-carbonyl)quinolin-4(1H)-one, aniline and diethyl ethoxymethylene malonate were used as precursors to synthesize ethyl 4-oxo-1,4-dihydroquinoline3-carboxylate, which was obtained in 50 percent yield. An addition reaction of alkyne followed by the elimination of ethanol was performed to obtain the 3-(1-phenyl1H-1,2,3-triazole-4-carbonyl)quinolin-4(1H)-one with ethynyltrimethylsilane and then carried out a click reaction with azides. All compounds obtained were characterized by 1H-NMR and 13C-NMR.

Membrane proteins are of undeniable importance for cell physiology across all domains of life and a loss of their function, e.g., due to mutations in their coding sequence, is almost always linked to disease. In humans, mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR), an ATP-gated anion channel in epithelia, give rise to cystic fibrosis (CF). Over 2100 mutations of the CFTR gene are known, however, their disease liability remains mostly undetermined. Causal therapies, i.e., small-molecule drugs that target CFTR itself, have improved the lives of people with the most common mutations (e.g. ΔF508, G551D) over the last decade. In contrast, many rare CF-phenotypic mutations are not eligible for these novel treatments and would benefit from in vitro evaluation of their molecular consequences. In vitro studies of membrane proteins are often complicated by the intrinsic hydrophobicity and aggregation susceptibility of this protein group. However, this can be avoided by using short membrane protein fragments corresponding to the smallest in vivo folding unit of the respective protein at the ER membrane. These model proteins can be easily genetically modified, expressed and purified, making them a suitable tool to pinpoint the effects of mutations. This thesis demonstrates the utility of such a reductionist model system: TM3/4, the second helical hairpin of CFTR’s transmembrane domain 1, was used to study protein folding with a focus on disease-causing missense mutations of CFTR, which may cause CFTR misfolding in vivo. TM3/4 purification was first optimized by using a thioredoxin tag, which allowed heat purification of the fusion protein even after initial purification steps. Optimal heat treatment for maximal protein purity and recovery were determined for TM3/4 and another helical hairpin, ATP synthase subunit c. Moreover, tertiary folding of a CF-phenotypic loop mutation, E217G, introducing a non-native GXXXG interaction motif was analyzed by single-molecule Förster resonance energy transfer (smFRET) in different lipid bilayer conditions, showing unusually increased stability in comparison to wild type (WT) TM3/4. Furthermore, smFRET was used in tandem with circular dichroism and fluorescence spectroscopy to assess the effect of a specific membrane lipid, cholesterol, on TM3/4 variants showing significant changes on secondary but not tertiary structure. Lastly, a mutant library of 13 TM3/4 mutants was established to perform drug screenings with CFTR correctors – a class of small molecules rescuing or preventing misfolding of CFTR. This screening study demonstrated that (i) not all CF-phenotypic missense mutations are locally misfolded at a lipid bilayer comparable to the ER membrane; and (ii) in vitro restoration of a native WT-like conformation of locally misfolded TM3/4 mutants is not only possible but different drug-mutant pairings can be identified related to folding rescue efficiency of a given corrector on a respective mutant. The latter identified drug-mutant pairings may lead to drug repurposing if the effect can be confirmed in cell culture experiments. In conclusion, the TM3/4 minimal model of CFTR and biophysical methods, such as smFRET, proved as versatile tools not only for investigation of mutation and lipid effects on membrane protein folding but also for drug screenings in a disease context.:1 INTRODUCTION 2 THEORETICAL BACKGROUND 2.1 MEMBRANE PROTEINS AND THEIR NATIVE ENVIRONMENTS 2.1.1 Membrane protein families and their role in human health 2.1.2 Fundamental folding models of α-helical membrane proteins 2.1.3 Co-translational folding at the ER supported by the translocon 2.1.4 Folding-relevant interactions within membrane proteins 2.1.5 Biological membranes and lipid classes 2.1.6 Physical properties of lipid bilayers impacting membrane proteins 2.1.7 Membrane models for in vitro studies 2.2 CYSTIC FIBROSIS AND CFTR 2.2.1 Pathology of cystic fibrosis 2.2.2 Structure and function of the CFTR channel 2.2.3 A minimal model of CFTR to study rare CF mutations 2.2.4 Missense mutations within the CFTR segmental model TM3/4 2.2.5 Novel modulator therapies for the treatment of cystic fibrosis 2.3 IN VITRO ASSESSMENT OF MEMBRANE PROTEIN FOLDING 2.3.1 Expression and purification of membrane proteins 2.3.2 Single-molecule FRET in single- and multi-well mode for protein folding 3 HEAT PURIFICATION OF TRX MEMBRANE PROTEIN FUSIONS 3.1 PREAMBLE AND SUMMARY 3.2 RESULTS AND DISCUSSION 4 IMPACT OF A CFTR LOOP MUTATION WITH ATYPICAL STABILITY 4.1 PREAMBLE AND SUMMARY 4.2 RESULTS AND DISCUSSION 5 EFFECTS OF CHOLESTEROL ON LOCAL CFTR FOLDING 5.1 PREAMBLE AND SUMMARY 5.2 RESULTS 5.2.1 Folding of TM3/4 hairpins in the presence of cholesterol 5.2.2 Folding of TM3/4 hairpins in the presence of Lumacaftor 5.2.3 Impact of Lumacaftor on membrane fluidity 5.3 DISCUSSION 6 CFTR CORRECTOR SCREENINGS WITH SINGLE-MOLECULE FRET 6.1 PRESCREENING TO IDENTIFY MISFOLDED TM3/4 VARIANTS 6.2 SCREENING OF MISFOLDED TM3/4 VARIANTS WITH CFTR CORRECTORS 7 CONCLUSIONS 8 OUTLOOK 9 MATERIALS AND METHODS 9.1 CONSTRUCT DESIGN OF HELICAL TRANSMEMBRANE HAIRPINS 9.2 PROTEIN EXPRESSION AND PURIFICATION 9.3 HEAT TREATMENT OF HELICAL TRANSMEMBRANE CONSTRUCTS 9.4 SINGLE-MOLECULE FRET EXPERIMENTS 9.4.1 Labeling of TM3/4 constructs 9.4.2 Liposome preparation and reconstitution of labeled protein constructs 9.4.3 Single-molecule FRET measurements in manual mode 9.4.4 Single-molecule FRET measurements in multi-well screening mode 9.5 CIRCULAR DICHROISM SPECTROSCOPY 9.5.1 Circular dichroism to determine protein heat stability 9.5.2 Circular dichroism to study protein structure in different lipid bilayers 9.6 FLUORESCENCE SPECTROSCOPY 9.6.1 Vesicle leakage assay to test lipid bilayer stability 9.6.2 Examining lipid bilayer fluidity with fluorescent probes 10 APPENDIX 10.1 GENERATION OF A TM3/4 MUTANT LIBRARY 10.2 TM3/4 SCREENINGS WITH CFTR CORRECTORS 10.2.1 SmFRET control screenings and supporting data 10.2.2 Extracted closed state fractions from smFRET screenings 10.2.3 DLS to measure vesicle integrity after corrector addition 11 REFERENCES 12 ACKNOWLEDGEMENTS 13 ERKLÄRUNG GEMÄß §5 ABS. 1 S. 3 DER PROMOTIONSORDNUNG / Membranproteine sind für die Zellphysiologie aller biologischen Domänen von unbestreitbarer Bedeutung und ein Verlust ihrer Funktion, z.B. durch Mutationen in ihrer kodierenden Sequenz, ist fast immer Auslöser von Krankheiten. Beim Menschen führen Mutationen im Gen für den Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), einen ATP-abhängigen Anionenkanal in Epithelien, zu Mukoviszidose (CF). Über 2100 Mutationen des CFTR-Gens sind bekannt – ob jedoch alle Mutationen tatsächlich CF auslösen, ist weitgehend ungeklärt. Kausale Therapien, d.h. niedermolekulare Medikamente, die auf CFTR selbst abzielen, haben in den letzten zehn Jahren die Lebensqualität von Menschen mit den häufigsten Mutationen (z.B. ΔF508, G551D) verbessert. Demgegenüber stehen jedoch viele seltene CF-phänotypische Mutationen, für welche diese neuartigen Behandlungen nicht zugelassen sind, wodurch diese Mutationen von einer In-vitro-Analyse ihrer molekularen Konsequenzen profitieren würden. In-vitro-Untersuchungen von Membranproteinen werden oft durch die intrinsische Hydrophobizität und Aggregationsanfälligkeit dieser Proteine erschwert. Dies kann jedoch vermieden werden, indem kurze Membranproteinfragmente verwendet werden, die der kleinsten in vivo Faltungseinheit des jeweiligen Proteins an der ER-Membran entsprechen. Diese Modellproteine können routiniert genetisch verändert, exprimiert und aufgereinigt werden, was sie zu einem geeigneten Werkzeug macht, um die Auswirkungen von Mutationen zu genau festzustellen. Diese Dissertation demonstriert die Nützlichkeit eines solchen reduktionistischen Modellsystems: TM3/4, das zweite helikale Haarnadel-Motiv der Transmembrandomäne 1 von CFTR, wurde verwendet, um Proteinfaltung mit Schwerpunkt auf krankheitsverursachende Missense-Mutationen von CFTR zu untersuchen, welche eine CFTR-Fehlfaltung in vivo verursachen können. Die TM3/4-Aufreinigung wurde zunächst durch die Verwendung eines Thioredoxin-Tags optimiert, der eine Hitzeaufreinigung des Fusionsproteins auch nach anfänglichen Reinigungsschritten ermöglichte. Die optimale Hitzebehandlung für maximale Proteinreinheit und -ausbeute wurde für TM3/4 und ein weiteres helikales Haarnadelprotein, die ATP-Synthase-Untereinheit c, bestimmt. Weiterhin wurde die tertiäre Faltung einer CF-phänotypischen Mutation, E217G, die ein nicht-natives GXXXG-Interaktionsmotiv einführt, mittels einzelmolekularem Förster-Resonanzenergietransfer (smFRET) in verschiedenen Lipiddoppelschichten analysiert, welche eine ungewöhnlich erhöhte Stabilität im Vergleich zum TM3/4-Wildtyp (WT) zeigte. Darüber hinaus wurde smFRET in Verbindung mit Circulardichroismus und Fluoreszenzspektroskopie verwendet, um die Wirkung eines spezifischen Membranlipids, Cholesterin, auf TM3/4-Varianten zu untersuchen, welches signifikante Auswirkungen auf die sekundäre, aber nicht auf die tertiäre Proteinstruktur hatte. Schließlich wurde eine Mutantenbibliothek von 13 TM3/4-Mutanten eingerichtet, um Wirkstoffscreenings mit CFTR-Korrektoren durchzuführen – einer Klasse kleiner Moleküle, die die Fehlfaltung von CFTR verhindern können. Diese Screening-Studie zeigte, dass (i) nicht alle CF-phänotypischen Missense-Mutationen lokal an einer Lipiddoppelschicht fehlgefaltet sind, die mit der ER-Membran vergleichbar ist; und (ii) die In-vitro-Wiederherstellung einer nativen WT-ähnlichen Konformation von lokal fehlgefalteten TM3/4-Mutanten ist nicht nur möglich, sondern es können auch verschiedene Wirkstoff-Mutanten-Paare identifiziert werden, die mit der Faltungsrettungseffizienz eines Korrektors auf eine bestimmte Mutante zusammenhängen. Die letztgenannten Wirkstoff-Mutanten-Paare können zu Drug-Repurposings führen, wenn die Wirkung in Zellkulturexperimenten bestätigt werden kann. Im Allgemeinen, haben sich das TM3/4-Minimalfaltungsmodell von CFTR sowie biophysikalische Methoden, wie z.B. smFRET, als vielseitige Werkzeuge nicht nur für die Untersuchung von Mutations- und Lipideffekten auf die Membranproteinfaltung, sondern auch für das Screening von Medikamenten im Krankheitskontext erwiesen.:1 INTRODUCTION 2 THEORETICAL BACKGROUND 2.1 MEMBRANE PROTEINS AND THEIR NATIVE ENVIRONMENTS 2.1.1 Membrane protein families and their role in human health 2.1.2 Fundamental folding models of α-helical membrane proteins 2.1.3 Co-translational folding at the ER supported by the translocon 2.1.4 Folding-relevant interactions within membrane proteins 2.1.5 Biological membranes and lipid classes 2.1.6 Physical properties of lipid bilayers impacting membrane proteins 2.1.7 Membrane models for in vitro studies 2.2 CYSTIC FIBROSIS AND CFTR 2.2.1 Pathology of cystic fibrosis 2.2.2 Structure and function of the CFTR channel 2.2.3 A minimal model of CFTR to study rare CF mutations 2.2.4 Missense mutations within the CFTR segmental model TM3/4 2.2.5 Novel modulator therapies for the treatment of cystic fibrosis 2.3 IN VITRO ASSESSMENT OF MEMBRANE PROTEIN FOLDING 2.3.1 Expression and purification of membrane proteins 2.3.2 Single-molecule FRET in single- and multi-well mode for protein folding 3 HEAT PURIFICATION OF TRX MEMBRANE PROTEIN FUSIONS 3.1 PREAMBLE AND SUMMARY 3.2 RESULTS AND DISCUSSION 4 IMPACT OF A CFTR LOOP MUTATION WITH ATYPICAL STABILITY 4.1 PREAMBLE AND SUMMARY 4.2 RESULTS AND DISCUSSION 5 EFFECTS OF CHOLESTEROL ON LOCAL CFTR FOLDING 5.1 PREAMBLE AND SUMMARY 5.2 RESULTS 5.2.1 Folding of TM3/4 hairpins in the presence of cholesterol 5.2.2 Folding of TM3/4 hairpins in the presence of Lumacaftor 5.2.3 Impact of Lumacaftor on membrane fluidity 5.3 DISCUSSION 6 CFTR CORRECTOR SCREENINGS WITH SINGLE-MOLECULE FRET 6.1 PRESCREENING TO IDENTIFY MISFOLDED TM3/4 VARIANTS 6.2 SCREENING OF MISFOLDED TM3/4 VARIANTS WITH CFTR CORRECTORS 7 CONCLUSIONS 8 OUTLOOK 9 MATERIALS AND METHODS 9.1 CONSTRUCT DESIGN OF HELICAL TRANSMEMBRANE HAIRPINS 9.2 PROTEIN EXPRESSION AND PURIFICATION 9.3 HEAT TREATMENT OF HELICAL TRANSMEMBRANE CONSTRUCTS 9.4 SINGLE-MOLECULE FRET EXPERIMENTS 9.4.1 Labeling of TM3/4 constructs 9.4.2 Liposome preparation and reconstitution of labeled protein constructs 9.4.3 Single-molecule FRET measurements in manual mode 9.4.4 Single-molecule FRET measurements in multi-well screening mode 9.5 CIRCULAR DICHROISM SPECTROSCOPY 9.5.1 Circular dichroism to determine protein heat stability 9.5.2 Circular dichroism to study protein structure in different lipid bilayers 9.6 FLUORESCENCE SPECTROSCOPY 9.6.1 Vesicle leakage assay to test lipid bilayer stability 9.6.2 Examining lipid bilayer fluidity with fluorescent probes 10 APPENDIX 10.1 GENERATION OF A TM3/4 MUTANT LIBRARY 10.2 TM3/4 SCREENINGS WITH CFTR CORRECTORS 10.2.1 SmFRET control screenings and supporting data 10.2.2 Extracted closed state fractions from smFRET screenings 10.2.3 DLS to measure vesicle integrity after corrector addition 11 REFERENCES 12 ACKNOWLEDGEMENTS 13 ERKLÄRUNG GEMÄß §5 ABS. 1 S. 3 DER PROMOTIONSORDNUNG

KCNE-Hilfsuntereinheiten assoziieren mit Spannungs-abhängigen K+-Kanälen und verändern dadurch deren subzelluläre Lokalisation, Regulation sowie deren biophysikalische Eigenschaften. Bei heterologer Expression interagiert KCNE3 mit mehreren Poren-bildenden K+-Kanal-Hauptuntereinheiten, deren Ströme dadurch stark modifiziert werden. Aufgrund dieser in vitro-Experimente wurden verschiedenste Funktionen von KCNE3 in den verschiedenen Geweben, wie Gehirn, Herz, Muskel, Kolon und Niere, vermutet. Außerdem wurden Variationen im kcne3-Gen mit menschlichen Skelettmuskelpathologien in Verbindung gesetzt (Abbott et al. 2001). In der gegenwärtigen Literatur wird die physiologische Funktion von KCNE3 eher als komplex und heterogen dargestellt. Auch die direkte Beteiligung von KCNE3 an Krankheiten ist immer noch spekulativ. Zur Untersuchung der physiologischen Funktion von KCNE3 in vivo sowie der potentiellen Rolle bei Krankheiten generierten wir ein kcne3-/- Mausmodell. Die vorliegende Arbeit unterstützt die kritische Rolle der KCNQ1/KCNE3-Kanäle beim Salz- und Flüssigkeitstransport über intestinale und respiratorische Epithelien. Insbesondere fanden wir für die KCNQ1/KCNE3-Heteromere eine basolaterale Lokalisation in Darm- und Trachea-Epithelzellen, wo sie die transepitheliale Cl--Sekretion über basolaterales Recycling von K+-Ionen sowie über Erhöhung der elektrochemischen Triebkraft für apikalen Cl--Austritt fördern. Da weder Veränderungen in der KCNQ1-Expressionsmenge noch in dessen subzellulärer Lokalisation festgestellt wurden, ist die durch KCNE3 verursachte Modifikation der KCNQ1-Kanaleigenschaften essenziell für die hier beschriebene physiologische Rolle im Intestinal- und Trachealtransport. Ferner wird von unserer Arbeit die postulierte Funktion von KCNE3-Heteromeren im Skelettmuskel, Herz und zentralen Nervensystem nicht unterstützt und erweckt somit erhebliche Zweifel über den Beitrag von KCNE3 zu menschlichen Krankheiten, die mit diesen Organen in Verbindung stehen. / When overexpressed in heterologous systems, KCNE3 is able to interact with several pore-forming K+ channel alpha subunits greatly modifying their currents. Based on these in vitro evidences, KCNE3 has been proposed to serve different roles in multiple tissues, including brain, heart, muscle, colon and kidney. Additional reports have also linked sequence variations in the KCNE3 gene to cardiac and skeletal muscle pathologies in human. Based on the literature, the overall picture of KCNE3 physiological function is rather complex and heterogeneous, and its direct involvement in pathologies is still speculative and far from being conclusively proven. In order to study the physiological role of KCNE3 in vivo and to address its potential pathological implications, we generated kcne3-/- mice. The present analysis of kcne3-/- mice strongly supports a crucial role of KCNQ1/KCNE3 channels in salt- and fluid secretion across intestinal and airway epithelia. In particular, we found that KCNQ1/KCNE3 heteromers are present in basolateral membranes of intestinal and tracheal epithelial cells where they facilitate transepithelial Cl- secretion through basolateral recycling of K+ ions and by increasing the electrochemical driving force for apical Cl- exit. Because the abundance and subcellular localization of KCNQ1 was unchanged in kcne3-/- mice, the modification of biophysical properties of KCNQ1 by KCNE3 is essential for its role in intestinal and tracheal transport. In addition, our work does not support the postulated role of KCNE3 heteromers in skeletal muscle, heart and CNS physiology, and raises considerable doubts concerning its implication in human pathologies which affect these tissues.

Die Ätiologie von entzündlichen Pankreaserkrankungen, insbesondere bei den idiopathischen Pankreatitiden, ist weitgehend noch nicht verstanden. In der folgenden Arbeit sollen immunologische und molekularbiologische Aspekte zu Pankreaserkrankungen unter Berücksichtigung eigener Untersuchungen dargestellt werden. Zu Beginn unserer Arbeit haben wir untersucht inwieweit immunologische Veränderungen an der Entstehung einer chronischen Pankreatitis beteiligt sind. Wir fanden eine systemische Aktivierung des zellulären Immunsystems, ohne dass sich Unterschiede zwischen idiopathischer und alkoholtoxischer Pankreatitis ergaben. Im folgenden haben wir uns mit dem molekularbiologischen Hintergrund von entzündlichen und malignen Pankreaserkrankungen beschäftigt. Eine genetische Modellerkrankung ist die hereditäre Pankreatitis, deren genetische Ursache 1996 mit der Entdeckung zweier Mutationen im kationischen Trypsinogen entschlüsselt wurde. Mit der Identifizierung einer neuen Mutation im kationischen Trypsinogen und deren funktionellen Charakterisierung konnten wir hier zum weiteren Verständnis dieser Erkrankung beitragen. Weitere Untersuchungen beschäftigten sich mit dem genetischen Hintergrund bei Patienten mit idiopathischer Pankreatitis. Bei etwa 30% dieser Patienten fanden wir ein abnormales Allel im Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Gen und bei einzelnen Patienten einen Polymorphismus im Serine Proteasen Inhibitor (SPINK1) Gen. Das zunehmende Wissen um genetische Veränderungen und deren Folgen setzt auch eine kritische Auseinandersetzung mit ethischen und rechtlichen Fragen voraus. Daher wurden während einer internationalen Konsensus Konferenz Richtlinien zum Umgang mit diesen Fragen erarbeitet. Die Assoziation von UGT1A7*3 Polymorphismus, welches ein Phase II Protein mit niedriger katalytischer Entgiftungsaktivität im Xenobiotika Stoffwechsel kodiert, mit dem Auftreten von Pankreaserkrankungen war Gegenstand weiterer Untersuchungen. Hierzu untersuchten wir Patienten mit alkoholischer chronischer Pankreatitis, Patienten mit einer SPINK1 Mutation und gesunde Kontrollen. Darüberhinaus betrachteten wir ein Kollektiv von Patienten mit einem Pankreaskarzinom. Unsere Ergebnisse belegen einen synergistischen negativen Effekt von exogenen Risikofaktoren (Alkohol, Nikotin) und genetischer Prädisposition. Die Rolle des oxidativen Stresses in der Genese von Pankreaserkrankungen wird damit untermauert. Erste therapeutische Ansätze aus den gewonnenen Erkenntnisses haben wir in einer prospektiven Studie mit einer immunmodulierenden und antioxidativ wirksamen Glutaminsubstitution bei Patienten mit akuter Pankreatitis gezeigt. Die Glutaminsubstitution führte zu einem besseren Krankheitsverlauf. / The etiology of inflammatory and malignat pancreatic disease are poorly understood. This thesis will discuss our results of immunological and genetic investigations in patients with inflammatory and malignat pancreatic diseases. Especially the background of idiopathic pancreatitis will be discussed. We started our investigations with immunological investigations and demonstrated an evidence for a systemic activated cellular immune system in patients with chronic pancreatitis irrespectively of the aetiology of pancreatitis. Further studies deal with the genetic background of pancreatitis. The discovery of the association between a mutation of the cationic trypsinogen gene and the hereditary pancreatitis was a milestone in the modern pancreatology. We contribute to the understanding of this disease by detecting a new mutation (D22G). We were able to functional characterise this mutation. Mutation of the activation peptides (D22G, K23R) are related to an increased release of trypsin in hydrolisation studies in vitro. In addition, our further investigations confirmed and extended the knowledge of the role of mutation in the CFTR gene and the SPINK 1 gene in patients with 'idiopathic' pancreatitis. Cognisant of the ethical and clinical responsibilities guidelines for the genetic testing and managing of patients with genetic diseases of the pancreas were developed. The low detoxification activity UGT1A7*3 polymorphism has been identified as a novel risk factor of pancreatic inflammatory and malignant diseases defining the interaction of genetic predisposition and environmentally induced oxidative injury. Based on this data we conducted a prospective, randomised clinical trial on the supplementation with glutamine in patients with acute pancreatitis shedulded for total parenteral nutrition. The administration of glutamine, which has been shown to have an immune-modulating and antioxidative capacity, was associated with a favourable clinical course of the patiens receiving glutamine.

<p>The cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP activated chloride channel in the apical membrane of epithelial cells, is defective in patients with cystic fibrosis (CF). Research efforts are focused on chloride channel function in order to find a cure for the disease.</p><p>Genistein increased chloride transport in normal and delF508-CFTR cultured airway epithelial cells without cAMP stimulation. Prior pretreatment with phenylbutyrate did not affect the rate of the genistein-stimulated chloride efflux in these cells.</p><p>S-nitrosoglutathione is an endogenous bronchodilator, present in decreased amounts in the lungs of CF patients. We studied the effect of GSNO on chloride (Cl-) transport in primary nasal epithelial cells from CF patients homozygous for the delF508-CFTR mutation, as well as in two CF cell lines, using a fluorescent Cl- indicator and X-ray microanalysis. GSNO increased chloride efflux in the CF cell lines and in primary nasal epithelial cells from CF patients. This effect was partly mediated by CFTR. If the cells were exposed to GSNO in the presence of L-cysteine, Cl- transport was enhanced after 5 min, but not after 4 h. GSNO may be a candidate for pharmacological treatment of CF patients. </p><p>Chloride transport properties of cultured NCL-SG3 sweat gland cells were investigated. The CFTR protein was neither functional nor expressed in these cells. Ca2+-activated chloride conductance was confirmed and the putative Ca2+-activated chloride channel (CaCC) was further characterized in term of its pharmacological sensitivity.</p><p>Corticosteroids, the primary treatment for asthma, cause necrosis/apoptosis of airway epithelial cells. It was investigated whether a newer generation of drugs used in asthma, leukotriene receptor antagonists, had similar effects. Both montelukast and dexamethasone, but not beclomethasone or budesonide induced apoptosis/necrosis in superficial airway epithelial cells. Montelukast and corticosteroids also caused decreased expression of intercellular adhesion molecule -1 (ICAM-1) in epithelial but not endothelial cells.</p>

Cystic Fibrosis (CF) is an autosomal recessive disease that arises from mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. The deletion of phenylalanine-508 (ΔF508-CFTR) is the most prevalent CF mutation and results in a misfolded protein that fails to exit the endoplasmic reticulum (ER). Previous studies demonstrated that mutation of a di-arginine based ER retention motif (R553AR555) in the first nucleotide binding domain (NBD1) rescues the trafficking defect of ΔF508-CFTR. We hypothesized that if the R553AR555 motif mediates retention of the ΔF508-CFTR protein, peptides that mimic this motif should antagonize mistrafficking mediated by aberrant exposure of the endogenous R553AR555 motif. We generated a peptide bearing the R553AR555 motif (CF-RXR) and conjugated it to the cell penetrating peptide Tat (CPP-CF-RXR) to facilitate intracellular delivery and investigated its efficacy in rescuing the mistrafficking and function of ΔF508-CFTR. Using a variety of biochemical and functional assays we demonstrate that the CPP-CF-RXR peptide is effective at increasing surface expression of ΔF508-CFTR in baby hamster kidney (BHK) and human embryonic kidney (HEK) cell lines. Furthermore, the increased surface expression is accompanied by an increase in its functional expression as a chloride channel. Using Ussing chamber assays, we demonstrate that the CPP-CF-RXR peptide improved ΔF508-CFTR channel function in respiratory epithelial tissues obtained from CF patients. Additionally, we investigated the effects of small molecules on mediating biosynthetic rescue of a ΔF508-CFTR construct bearing the additional mutations R553K and R555K (ΔFRK-CFTR) to inactivate the R553AR555 motif. Interestingly, mutation of the R553AR555 motif exerts an additive effect with correctors VRT-325 and Corrector 4a. Taken together, our data suggests that abnormal accessibility of the RXR motif present in NBD1 is a key determinant of the mistrafficking of the major CF causing mutant.

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