BACKGROUND: Cystic fibrosis (CF) patients grow poorly and tend to be malnourished. They frequently suffer from lung infections necessitating the repeated use of antibiotics. AIM: This study was conducted to determine whether supplementation with a probiotic Lactobacillus reuteri (L. reuteri) could reduce the incidence and duration of lung infections, and whether this would impact on their anthropometric data. The secondary purpose was to compare the nutritional status of the CF patients attending CF clinics in Kwazulu-Natal (KZN) with CF patients attending CF clinics in Cape Town (CT). METHODS: Twenty three CF patients 6-31 years of age from 2 CF clinics in Kwazulu-Natal started the study although only 16 patients completed it. The study was a randomized, double blind, placebo controlled crossover trial with six months on placebo and six months on probiotic. Weight, height, mid arm circumference (MAC), triceps skin fold thickness (TSF), forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) were measured, sputum collected and a symptom diary completed over the 12 month period. Anthropometric data of CF patients attending CF clinics in CT was obtained from the publication by Westwood & Saitowitz (1999). RESULTS: Compliance with taking the L. reuteri was poor. Most took only 50% of the required daily dose. Probiotic supplementation showed a slight (non significant) trend to improve FEV1 and FVC, while no significant difference could be seen in the number and duration of the lung infections. Sputum analysis showed a non significant trend towards the probiotic reducing the number of bacteria in the sputum. There was a significant reduction of symptoms for fever, running nose, sore throat and ear ache while on placebo. There was a significant increase in weight gained off probiotic compared to the probiotic period. The changes in height, weight for age (WFA) percentiles, height for age (HFA) percentiles, WFA and HFA Z-scores, percentage expected weight for age and percentage expected height for age all showed no difference whether on or off probiotic. Over half the CF children in the KZN clinics were underweight for their actual height compared to one third in the CT clinics with a higher number of subjects below the 5th percentile for MAC and TSF readings compared to CT. CONCLUSION: Due to a small sample size and poor compliance no firm conclusions could be drawn. However a slight (non significant) improvement could be seen in favour of the probiotic for FEV1, FVC, and sputum analysis. Although all other findings were not significantly different it would be of benefit to carry out further investigation with improved compliance with the probiotic to see if the parameters set out above could be improved. The KZN and CT CF groups were comparable and the nutritional status of CF patients on KZN was well below that of the CT CF clinics and further monitoring would need to be carried out.

Cystic Fibrosis (CF) is a common life-shortening autosomal recessive disease that affects over 100.000 people worldwide people worldwide. It is caused by mutations in the CF trans-membrane conductance regulator (CFTR) gene, that encodes for a membrane channel localized at the apical surface of epithelial cells where it has a crucial role in the secretion of chloride and bicarbonate. Over 2100 different CFTR mutations have been reported and among the pathogenic once the most common is F508del, located in the nucleotide-binding domain 1 (NBD1). F508del is a three-nucleotide deletion that results in the loss of a phenylalanine at position 508 in the protein and in the consequent CFTR degradation by the ubiquitin-proteasome system. Different attempts to correct F508del-CFTR gene were made using genome editing approaches, however deletions like F508del remain difficult to be repaired. Several studies reported that additional mutations (revertant mutations) in the F508del-CFTR gene can rescue both CFTR folding and activity, suggesting a potential novel strategy to correct F508del. For this reason, the first aim of this work was the identification of novel F508del-CFTR revertants that can rescue CFTR localization and function. We generated a library of mutants introducing random substitutions into the F508del-CFTR gene. Revertant mutations were isolated based on their ability to rescue the presence of CFTR at the plasma membrane (PM) in HEK293T cells and identified by Sanger sequencing. Restoration of CFTR maturation, localization, and function of the identified revertants was evaluated by western blot, flow cytometry analysis and YFP assay, reaching levels similar to the wild type CFTR. Then we used CRISPR-Cas technology to introduce selected revertant mutations, such as I539T, R553Q, G550E, R555K and R1070W, in the endogenous F508del-CFTR gene. Adenine and cytosine base editors (ABE and CBE) allow the insertion of the desired base conversion without the formation of double strand breaks. Efficient editing was evaluated through Sanger sequencing, reaching up to 60% of base conversion. CFTR rescue at the PM in edited cells was analyzed by flow cytometry showing different degrees of recovery compared to the wild type CFTR. In this work, we confirmed that revertant mutations can rescue F508del CFTR localization and function. In addition, we demonstrated that CRISPR-base editors are valid tools to introduce these mutations in the endogenous F508del-CFTR gene, leading to a permanent correction. The proposed strategy could overcome the limits that genome editing strategies faced till now in the correction of F508del, providing a new potential therapeutic approach to treat CF.

Master of Science / Biochemistry and Molecular Biophysics / John M. Tomich / NC-1007 (CK₄-M2GlyR) (PARVGLGITTVLTMTTQSSGSRAKKKK) is a synthetic peptide modeled after the second transmembrane segment of the spinal cord glycine receptor’s α-subunit, and has demonstrates the capacity to oligomerize to form transmembrane channels with Cl[superscript]- permselectivity. While studies into the effects of truncation on both CK[subcript]4 (C-terminal tetra-lysl adducted) and NK[subscript]4 (N-terminal tetra-lysl adducted) led to more control over solution aggregation in the NK[subscript]4 variant, the work presented explore whether C-terminal sequential substitutions with a tryptophan residue could similarly stabilize the aqueous structure in monomeric form or further define the pore registry in such a way as to promote an increase ion permeability. Tryptophan was substituted for amino acids in the 18[superscript]th, 19[superscript]th, 20[superscript]th, and 21[superscript]st positions of the peptide sequence (SSGS, respectively), and changes in aggregation profiles, secondary structure, and channel ion permeability were observed. Synthesized peptides show circular dichroism spectral profiles indicating that the studied tryptophan substitutions did not result in a reduction of the characteristic helicity of the peptide; however, the tryptophan substitution also did little to decrease solution aggregation as demonstrated by comparative studies by reverse-phase high- performance liquid chromatography. All peptides demonstrated channel activity, directly measured by recordings of transepithelial short-circuit current. with profiles that suggest trends in electrostatic interactions and membrane registry relative to substitution position. One peptide in particular, NC-1007 S21W displayed atypical activity, which could not be effectively described by the standard Hill-based model but may be indicative of an ill-defined registry due to the substituted peptide’s proximity to another strongly pore-defining residue. Further studies in the effects of sequence modification to channel-forming peptides will elucidate how sequences may be altered to optimize synthetic peptide solubility, resistance to in-solution aggregation, and ability to form selective and permeable ion channels. The understanding gained from this study will improve our ability to develop peptides that could serve as a therapeutic treatments for a number of endogenous channelopathies.

Call number: LD2668 .T4 1965 B71 / Master of Science

Clinical research in cystic fibrosis (CF) requires study endpoints that are sensitive to airways disease, repeatable and non-invasive. Despite significant advances in the treatment of CF, lung function assessments continue to rely on the forced expiratory volume in 1 second (FEV1). Although simple to perform, it lacks sensitivity, is difficult for younger subjects, and changes over time. An alternative method of assessing lung physiology is to derive measures of ventilation heterogeneity from inert gas washout tests. In early lung disease, measures of gas mixing appear to be more sensitive than spirometry. In addition, since only tidal breathing is required, they are more physiological and are more straightforward for younger subjects. Widespread use has been impaired by the lack of a robust and cost effective gas analyser technology. The work presented in this thesis concerns the adaptation, validation and then use of a novel gas analyser (Innocor) in a clinical system for the performance of multiple breath washouts. Lung clearance index (LCI), a simple measure of ventilation heterogeneity, has been calculated from washouts in 52 adults with CF and 50 healthy controls. LCI was more sensitive to disease than FEV1 in CF, being elevated in 11 of the 12 CF patients with normal spirometry. In healthy subjects, LCI has been shown to be repeatable and reproducible, with a narrow range of normal that is stable over a wide age range. In a separate study of 19 patients, LCI has also been shown to improve with treatment of an exacerbation in CF. Correlation with changes in other biochemical (serum CRP, peripheral blood white cell count, sputum IL-8, sputum neutrophil) clinical (symptom score) or structural (computed tomography) markers was poor. Short term change in LCI has also been demonstrated in CF patients in response to chest physiotherapy, although there was considerable heterogeneity of response in terms of both LCI and volume of lung ventilated by tidal breathing (as measured by washout functional residual capacity). In addition to LCI, multiple breath phase III slope analysis has been performed on washouts of CF patients and healthy controls, and this has been compared to other measures of lung physiology. Proposed measures of convective and diffusive gas mixing have been shown to be unreliable in CF. These studies have also been the first to demonstrate multi-centre use of washout tests as endpoints. The technology described here offers the possibility of a simple and reliable system for performing multiple breath washouts, though at present it is not available commercially. The studies have added to the understanding of the utility and reliability of washout tests, as well as some of their limitations. It is hoped that in future LCI will be an important clinical endpoint in therapeutic intervention studies in CF, and that it will also offer new ways to follow changes in lung physiology in other diseases.

Cystic fibrosis (CF) lung disease is characterised by early airways infection and inflammation, chronic suppuration, frequent infective exacerbations and an increased influx of acute, and chronic inflammatory cells. The inflammatory process involves activation of many cell types including neutrophils, macrophages and epithelial cells, and leads ultimately to the development of progressive respiratory failure and death. Accurate assessment of the inflammatory process is a crucial part of disease monitoring and should allow appropriate evaluation of therapeutic interventions so as to maximize control of the respiratory sequelae of the disorder. Lung function markers such as FEV1 are insensitive and indirect. Direct but invasive methods such as fibreoptic bronchoscopy and biopsy are limited in application, repeatability and safety. Non-invasive methods of assessment are, therefore, attractive. Exhaled Breath Gases, Exhaled Breath Condensate and Induced Sputum provide potential for such measures. These techniques are safe, simple, repeatable and could assess all airways and can be used in children as young as 6 years. We hypothesised that biomarkers of inflammation in Cystic Fibrosis Lung Disease are measurable in samples collected noninvasively, and can be developed into clinically useful assays. These assays would have the ability to reflect the level of inflammation in the CF lungs as well as holding the potential to act as surrogate markers of CFTR function. Methods Non-invasive markers of inflammation in Cystic Fibrosis lung disease Methods. Exhaled breath gases, exhaled breath condensate, bronchoalveolar lavage fluid and induced sputum were investigated using a number of analysis techniques to identify the markers which best discriminated CF from non CF subjects. Analysis techniques used were electrochemical cells, chemiluminescene, ELISA, EIA, ion selective probes and mass spectrometry. Results Markers found to discriminate CF from non CF subjects were EBC pH and ammonium, and 38 proteomic markers were found in induced sputum. 21 proteomic markers were found in bronchoalveolar lavage fluid. One biomarker has been identified with confidence, Calgranulin A. Discussion A large component of the work of this thesis was focussed on exhaled breath condensate. Two markers, pH and Ammonium were different between the CF and control groups. The measurement of EBC pH and ammonium as markers of inflammation should be used in future gene therapy trials as they are cheap, quick and simple to perform Using clean techniques free from contamination, no proteins are repeatedly detectable in EBC using highly sensitive SELDI techniques. This technique reflects the highest sensitivity of any available proteomics instrument and therefore until new technologies become available, it would be incorrect to assay any proteins in EBC. The induced sputum proteomics study identified 38 independent markers of CF lung inflammation Therefore, sampling by collection of induced sputum should be used in gene therapy trials. The endpoints should be assessed by a combination of SELDI as an endpoint and by ELISA where this is available. The marker Calgranulin is likely to report on neutrophil recruitment to the lung. It is anticipated that this will be a sensitive marker of inflammation in the lung and it also has the potential to report on successful of gene transfer as it is raised in heterozygote carriers as well as homozygotes with CF. Therefore, the non-invasive technique induced sputum coupled to proteomic analysis would have the ability to reflect the level of inflammation in CF subjects and may also report on CFTR function.

Class of 2012 Abstract / Specific Aims: We sought to determine the influence of genetic variation of ADRB2 on the airway response to albuterol in patients with CF when compared to matched healthy controls at baseline and at 60 minutes following the administration of albuterol (2.5mg diluted in 3ml normal saline). Methods: Baseline pulmonary function (forced vital capacity, FVC, forced expiratory flow in 1-second, FEV1, mid-maximal expiratory flow, MMF, and forced expiratory flow at 50% of the FVC) was assessed in 17 patients with CF and 31 healthy subjects. Main Results: As expected, the healthy group had higher baseline pulmonary function when compared to the CF group (FVC=97±3 vs. 83±5; FEV1=95±3 vs. 72±6; MMF=90±4 vs. 54±8, % predicted for healthy and CF, respectively, mean±SE, p<0.05 for all. We compared Arg16Arg to Arg16Gly/Gly16Gly subjects. There was no effect of genotype on the response to albuterol in healthy subjects. However, in the CF group, we found that the Arg16Arg group (n=6) had an attenuated response to β-agonist when compared to the Gly-containing group (n=11) (FVC=0±0.9 vs. 6±3: FEV1=3±1 vs. 7±4: MMF=12±3 vs. 12±5 % change, for Arg16Arg and Gly-containing groups, respectively, p<0.05 for FVC, p=0.06 for FEV1). Conclusions: These results demonstrate a differential response to β-agonists according to genetic variation of the ADRB2 at amino acid 16. Due to the differences in FVC and FEV1 but not in MMF, these data suggest that the genetic difference in airway function is primarily in bronchodilation of the larger airways.

Class of 2010 Abstract / OBJECTIVES: Cystic fibrosis (CF) is a disease that adversely affects the lung resulting in a reduction of lung diffusion. Stimulation of the β2 adrenergic receptors results in mucocilliary clearance, and therefore, lung diffusion. We sought to determine the influence of an inhaled β-­‐agonist on the diffusing capacity of the lungs for carbon monoxide (DLCO), alveolar-­‐capillary membrane conductance (DM), pulmonary capillary blood volume (Vc), and peripheral oxygen saturation (SaO2) in subjects with CF and compare the data to matched healthy subjects. METHODS: To determine this we recruited 20 healthy subjects and 18 subjects with CF (age=23±7 vs. 24±4years, ht=168±8 vs. 174±12cm. wt=64±16 vs. 70±13kg, BMI= 23±4 vs. 23±3kg/m2, FEV1= 72±27 vs. 92±12%pred., VO2peak = 45±25 vs. 99±24%pred., P<0.05 for FEV1 and VO2peak, mean±SD) for the study and measured DLCO, DM, Vc and SaO2 before and 30, 60, and 90 minutes following the administration of inhaled albuterol. RESULTS: Within the healthy subjects, there were no differences in DLCO, DM, Vc, DM/Vc at baseline or in response to albuterol according to genetic variation of the ADRB2 at amino acid 27. Within the CF group, the Glu27Glu/Gln27Glu group had higher DM/Vc when compared to the Gln27Gln group at baseline. Both genotype groups had a significant decline in Vc and a significant improvement in DM/Vc and SaO2 in response to albuterol, but not in DLCO or DM. CONCLUSIONS: These results suggest that there are differences in lung diffusion and peripheral SaO2 according to genetic variants of the ADRB2 at position 27 and could play a potential role in treatment options.

Pseudomonas aeruginosa (PA) infections in Cystic Fibrosis (CF) patients are not easily cleared due to the conversion from a nonmucoid to a mucoid phenotype. Alginate is an acetylated exopolysaccharide produced by mucoid PA that is responsible for increased resistance to antibiotics, host phagocytic killing, and propagating biofilm formation. Understanding the interaction between PA and host cells is critical to understanding chronic infection and inflammation in CF. In order to investigate this, we used A549 pulmonary epithelial cells and murine alveolar macrophages (MH-S) to examine host response to nonmucoid versus mucoid PA infection. Adhesion assays in A549 pulmonary epithelial cells revealed that mucoid PA mutants adhere poorly compared to their nonmucoid counterparts. Similarly, phagocytosis assays using MH-S infected with PA revealed that mucoid PA are increasingly resistant to phagocytosis. The alginate acetylation mutant FRD1175 is more susceptible to phagocytic killing than alginate+ FRD1. Adherence and phagocytosis of mucoid FRD1 was increased by increasing the multiplicity of infection (MOI) from 50:1 to 500:1. Furthermore, confocal microscopy revealed that mucoid PA are inherently less inflammatory than nonmucoid strains in both A549 and MH-S. Increasing the MOI of mucoid FRD1 from 50:1 to 500:1 significantly increased caspase-1 activation in MH-S but not in A549, revealing that intensity of inflammatory signaling by epithelial cells is likely independent of increased adherence. FRD1175 infection in both A549 and MH-S revealed that alginate acetylation plays a significant role in reducing inflammasome activation. Western analysis revealed that PA does not actively induce TGF-β secretion by A549 epithelial cells. Similarly, NF-κB expression was reduced in both A549 and MH-S when infected with mucoid FRD strains, but not PA from the PAO background, suggesting FRD strains have accumulated additional mutations facilitating escape of inflammation. MH-S treated with cytochalasin D to block phagocytosis were still able to activate NF-κB signaling, suggesting NF-κB activation is adherence but not phagocytosis dependent. These data increase our understanding of the various mechanisms in which mucoid PA is able to evade host immune defenses and provides insight into potential therapies to treat PA infections.

Cystic Fibrosis (CF) is the most common hereditary genetic disorder among Caucasians. Pseudomonas aeruginosa is a major cause of morbidity in cystic fibrosis patients. Chronic infection with P. aeruginosa eventually occurs and is associated with a switch to biofilm formation of the bacteria. The symptoms and pathology of acute and chronic P. aeruginosa infections differ greatly. The first line of defense within the lung is the physical barrier of the lung epithelia. The examination of established biofilm interactions with lung epithelia is difficult. Here, I use the Calgary Biofilm Device co-culture system to conduct the concurrent analysis of established biofilms and planktonic bacteria with A549 lung cells. Comparison of P. aeruginosa biofilm and planktonic bacteria’s effects on A549 lung cells showed that planktonic bacteria caused more A549 cell rounding and death, while biofilm stimulated more IL-8 release by epithelial cells. Biofilm was shown to secrete significantly more Pseudomonal Elastase than planktonic, causing A549 morphological changes and loss of tight junctions. The antimicrobial peptide LL-37 was shown to differentially affect biofilm and planktonic bacteria. LL-37 caused a decrease in twitching of planktonic bacteria and exposure to LL-37 for 48 hours resulted in a decrease in elastase secretion likely due to down-regulated type 2 secretion. When established biofilms were compared with newly adherent biofilms, young biofilms were shown to have characteristics similar to both planktonic bacteria and mature biofilms. From this data we can follow the pattern of bacterial virulence as P. aeruginosa transitions from the planktonic mode of growth to the eventual mature biofilm that is associated with chronic infection. In conclusion, this study provides the foundation for a co-culture system that can be used to study the host-pathogen interactions of mammalian epithelia with established P. aeruginosa biofilms. The future adaptations of this model will better represent the in vivo characteristics of chronic lung infection to delineate ongoing virulence mechanisms of the bacteria causing host cell stimulation and damage. / May 2016