Background: Lung function is a highly heritable trait. So far there is limited knowledge of the genetic factors that influence lung function. Vascular endothelial growth factor A (VEGF-A) is expressed in the lung at high levels and is known to play a role in angiogenesis and lung remodelling, both in utero and throughout life. A candidate gene study was carried out in order to investigate the role of variants within the VEGF-A gene in determining lung function in childhood and adult life.Methods: Using available longitudinal data previously collected for an unselected birth cohort (Manchester Asthma and Allergy Study-MAAS) the relationship between lung function and single-nucleotide polymorphisms (SNPs) in VEGF-A was assessed. Replication studies were performed in cross-sectional studies of adults from Manchester and children with asthma from Croatia, in whom FEV1/FVC ratio was measured using spirometry. The potential functional roles of two consistently associated SNPs were then further investigated. Finally, using the genome-wide data generated in the discovery cohort (MAAS) I assessed why associations between VEGF-A and lung function had not been reported in recent genome-wide association studies of lung function.Results: Two VEGF-A SNPs, rs10434 and rs3025028, were significantly associated with lung function at multiple ages in a discovery population (MAAS). Subjects with a GG genotype for either SNP had significantly diminished lung function compared to subjects with other genotypes. These findings were replicated in two additional populations (631 parents of children participating in MAAS and in 410 Croatian children with physician-diagnosed asthma aged 6-18 years). SNP rs10434 is located in the 3’UTR and based on its location I hypothesised that it may affect mRNA stability. No significant difference in the rate of VEGF-A mRNA degradation was found between GG and the AA homozygotes. SNP rs3025028 is an intronic SNP in a close proximity to the splice site involved in alternative splicing which generates two different isoforms of VEGF-A; I therefore tested the hypothesis that a change of base at this position could affect the splicing mechanism and cause a change in the ratio of the isoforms. Western blot analysis was used to demonstrate a difference in the ratio of the splice variants VEGF-A165b and total VEGF-A165 (relative to a reference sample) between genotype groups. The VEGF-A165b/panVEGF-A165 ratio was significantly higher at birth (cord plasma), in school-age children and in adults amongst CC compared to GG homozygotes at rs3025038 (p<0.03). Finally, the genome-wide data for the discovery cohort showed that the region containing VEGF-A was not well targeted by either genotyped or imputed SNPs in genome-wide arrays. Conclusion: Evidence was provided to demonstrate that variants within the VEGF-A gene are significantly associated with lung function in both children and adults. Furthermore, data was presented to support a functional role for one of the SNPs (rs3025028). I investigated why associations between VEGF-A and lung function had not previously been reported in recent GWAS and concluded that the region containing VEGF-A was poorly covered by all of the currently available arrays.

Since the first modern investigations into Egyptian mummies in the 1970s, anthracosis and silicosis have regularly been found in mummified lungs (Tapp, 1975; Walker et al, 1987). Anthracosis, lung irritation caused by carbon particles, is well researched in modern populations but very little is known about the disease in ancient times. Similarly, little is known about the prevalence of silicosis, caused by the inhalation of particles of silicon, in ancient times. It has been assumed that carbon was inhaled through the combustion of fuel for cooking and illumination whilst silicon came from the desert environment.This study aims to test these assumptions by characterising the shape, size and elemental composition of the organic and inorganic particles contained within ancient lung tissue. When these particles are compared against surrogate carbon and silicon particles, it may be possible to identify them and reveal their aetiology.Surrogate carbon particles were produced through controlled combustion of fuels the ancient Egyptians are likely to have used. The modern silica containing sand was collected from various archaeological sites in Egypt. A sonication method was used to extract particles from ancient tissue. After extraction, individual ancient particles were isolated and examined for size and shape analysis using light microscopy. The surrogate particles were examined in the same manner. The particles were then imaged using environmental scanning electron microscopy (ESEM) and elemental profiles determined by energy dispersive X-ray analysis (EDAX). Bulk analysis by mass spectrometry was then employed to qualitatively and quantitatively analyse the elements contained within ancient lung particles and the modern surrogates. Electron probe micro-analysis (EPMA) was used to map the deposition and elemental composition of inorganic compounds in sections of ancient lung. Further information on the bonds and chain length of soots were obtained through FTIR and Raman spectroscopy.Results have shown the presence of anthracosis and birefringent particles in all ancient lung tissues examined by this study. Both organic and inorganic ancient particles have been found to be respirable (ie, less than 10 microns in diameter) and were present in the lung pre-mortem. EDX and ICP-MS results show the inorganic particles to consist of aluminium silicates (sand) and calcium carbonate (limestone). FTIR and Raman spectroscopy were not accurate enough to detect the ancient or surrogate soot bonds and were not suited to this study.

Improved radiotherapy (RT) outcomes may be facilitated through monitoring of physiological processes implicated in radio-resistance such as proliferation. To this end, we studied 16 patients with non-small cell lung cancer with dynamic 3'-deoxy-3'-fluorothymidine (FLT) PET-CT before and after a week of radical RT. In absence of changes in primary tumour volume manually delineated on CT, RT induced a significant, moderately variable decrease in maximum and mean standard uptake values (SUVmax and SUVmean) of the order of 25%. Metastatic nodes showed a larger relative decrease in uptake approximating 40% associated with volumetric regression and only partially accountable by partial volume effect. Implementation of different segmentation approaches including manual delineation by a second operator and PET-based semi-automatic algorithms [two fixed thresholds, 2/3-cluster Fuzzy C-means (FCM-2, FCM-3) and 2/3-cluster fuzzy locally adaptive Bayesian algorithm (FLAB-2, FLAB-3)] yielded substantially different volumes and SUVs but consistent SUV responses. Reproducibility comparison favoured manual delineation, while thresholding delivered poor volumetric robustness and no apparent SUV reproducibility advantage over SUVmax or SUVpeak. FCM-2/FLAB-2 demonstrated intermediate reproducibility. In contrast to anatomical volumes, metabolic volumes exhibited significant increases with treatment, which for FLAB-2 correlated with changes of intratumoural uptake heterogeneity quantified by the coefficient of variation. Normal tissue analysis revealed an anterior-posterior gradient of lung uptake and an association of baseline marrow SUV with type/timing of neo-adjuvant chemotherapy. RT induced a dramatic (≈-76%), sharply demarcated marrow SUV decline in response to a minimum of 5Gy and a small (≈-20%), consistent decline in normal lung SUV. Kinetic analysis revealed a significant increase in the tumour delivery constant K1 (+32%) and a decrease in Ki/K1, larger (-36%) and more variable than the Ki (-26%) and SUV responses. Furthermore, despite baseline independence, we found a strong negative correlation between Ki/K1 and K1 at the response level. Kinetic analysis of the most uptake-avid tumour cluster extracted with FCM-3 yielded similar results with attenuated changes in delivery and retention. Overall, we found that RT induces early measurable changes in lung tumour FLT uptake. Spatial analysis indicated a variable dissociation of anatomical and metabolic volumes, while temporal analysis showed a variable antagonistic effect on delivery and phosphorylation, indicating that SUV analysis may misrepresent the magnitude and variability of RT anti-proliferative effect.

Small Cell Lung Cancer (SCLC) is a very aggressive neuroendocrine tumour of the lung, which demonstrates a 5 year survival of only 10% for extensive stage disease (20-30% for limited stage), with only modest improvement over the last few decades. Identification of new molecular diagnostic and therapeutic targets is thus imperative. Previous efforts in identifying molecular changes in SCLC by gene expression profiling using microarrays have facilitated disease classification but yielded very limited information on SCLC biology. Previous DNA studies have been successful in identifying several loci important to SCLC. However the low resolution of conventional chromosomal Comparative Genomic Hybridization (CGH) has limited the findings to large chromosomal regions with only a few specific candidate genes discovered to date. Thus, to further understand the biological behaviour of SCLC, better methods for studying the genomic alterations in SCLC are necessary. This thesis highlights the development of array CGH technology for the high resolution dissection of aneuploidy in cancer genomes and the application of this new technology to the study of SCLC. I present the development of the first whole genome CGH array which offered unprecedented resolution in the profiling of cancer genomes allowing fine mapping of genes in a single experiment. Through application of DNA based analysis in conjunction with integrated expression analysis and comparison of SCLC to less aggressive non-small cell lung tumours I have identified novel patterns of pathway disruption specific to SCLC. This included alteration to Wnt pathway members and striking patterns of cell cycle activation through predominantly downstream disruption of signalling pathways including direct activation of the E2F transcription factors, which are normally repressed by the Rb gene. Analysis of targets of the E2F/Rb pathway identified EZH2 as being specifically hyper-activated in SCLC, compared to NSCLC. EZH2 is a polycomb group gene involved in the control of many cellular functions including targeted DNA methylation and escape from senescence in hematopoietic stem cells. Taken together these results suggest that in SCLC, downstream disruption may replace multiple upstream alterations leading to activation independent of a specific mitogenic pathway, and that EZH2 represents a potentially important therapeutic target. / Medicine, Faculty of / Pathology and Laboratory Medicine, Department of / Graduate

Infants with bronchopulmonary dysplasia (BPD), showed impaired body growth when compared to control infants. In terms of changes in the biochemical composition of the lung, BPD infants had higher DNA, soluble protein, collagen and desmosine contents as well as increased concentrations of DNA, collagen and desmosine in their lungs when compared to the growth patterns obtained for the lungs of control infants. Pathologically BPD was classified into 4 grades. Grade I BPD, was a phase of acute lung injury, grades II and III were proliferative phases. In grade IV BPD, lung structure returned towards normal. Evidence of fibrosis was seen by a significant increase in collagen concentration in grades II and III while desmosine concentration was seen to increase in grades III and IV suggesting that the increase in collagen and desmosine contents in the lungs of BPD infants may be controlled by two different mechanisms. Collagen type I/III ratio was seen to decrease progressively from grade II to grade IV BPD in comparison to age matched controls, indicating a higher proportion of type III collagen in the lungs of infants with BPD. From the clinical analysis and the results obtained from discriminant analysis procedure, it was seen that there was a high degree of correlation between the continuation of the disease and collagen accumulation in the lungs suggesting that pulmonary fibrosis with excessive collagen accumulation is an integral part of BPD. This fibrotic process seemed to correlate significantly with assisted ventilation and high oxygen supplementation received by the infants, but it was difficult to assess the individual contribution of the two treatments in the pathogenesis of BPD. Other variables such as severity of the initial disease and the length of survival of the infants, made the assessment of individual contribution much more difficult. / Medicine, Faculty of / Pathology and Laboratory Medicine, Department of / Graduate

This study examined the effects of epinephrine, norepinephrine, AVP and ACh on fluid movement by the lungs of the late-term guinea pig fetus. Catecholamines and AVP are secreted in high amounts by the fetus during delivery, and could be important with respect to fetal lung fluid removal; this event is vital at the time of birth. The lungs were supported in vitro for a duration of three hours, and production rates were measured using a dye-dilution technique. The average resting production rate in terms of ml/kg‧h declined with gestational age (54-67 days gestation; n=171). There was a lesser decline in the average resting production rate in terms of ml/h. The average production rate of untreated preparations in the first hour was 1.60 ± 0.26 ml/kg body weight per hour, and rates did not change significantly during the remaining two hours of experimentation (n=30). This rate is comparable to those reported from chronically catheterized fetal sheep. Treatment was administered during the second hour of experimentation, following an ABA design. Lungs (n=36) were transferred to fresh Krebs-Henseleit saline containing one of the following concentrations of epinephrine: (a) 10‾⁵ M; (b) 10‾⁶ M; (c) 10‾⁷ M; (d) 5 x 10‾⁸ M; (e) 10‾⁸ M; and (f) 10‾⁹ M. With the exception of the top dose, epinephrine treatment caused an immediate reduction in fluid secretion, or fluid reabsorption. Sodium followed the movement of water in all cases. The effect of epinephrine at 10‾⁷ M was maximal, and the threshold dose for epinephrine was calculated at 1.78 x 10‾¹¹ M. Phentolamine and propranolol had no effect in control preparations. However, phentolamine completely blocked the effect of epinephrine, whereas propranolol was ineffective. Isoproterenol had no effect on pulmonary fluid production. Alpha-adrenergic receptors apparently mediate the effect of epinephrine on pulmonary fluid movement in the fetal guinea pig lung. This conclusion is different from that obtained in fetal sheep, in which beta-adrenergic receptors are utilized. A possible synergism between epinephrine and AVP was examined. Lungs (n=12) were transferred to fresh Krebs-Henseleit saline containing either (a) 0.6 mU/ml AVP, or b) 0.6 mU/ml AVP combined with epinephrine at 10‾⁷ M. Treatment with AVP caused a slow, prolonged reduction in fluid production. Treatment with AVP together with epinephrine did not demonstrate synergism. The effect of norepinephrine (NE) was examined. Lungs (n=36) were transferred to fresh Krebs-Henseleit saline containing one of the following concentrations of NE: (a) 1.24 x 10‾⁵ M; (b) 1.24 x 10‾⁶ M; (c) 1.24 x 10‾⁷ M; (d) 5.24 x 10‾⁸ M; (e) 1.24 x 10‾⁸ M; and (f) 1.24 x 10‾⁹ M. In all preparations, treatment with NE resulted in an immediate reduction in fluid production, and reabsorptions were observed at the higher doses. Sodium followed the movement of water in every case. The threshold dose was calculated at 3.16 x 10‾¹⁰ M. Phentolamine blocked the effect of NE, reinforcing the importance of pulmonary alpha-adrenergic receptors in the fetal guinea pig. There was no relationship between age and degree of response with treatment of either epinephrine or NE, but fetuses under 78.0 g did not respond to NE. The effect of ACh was examined. Lungs (n=24) were transferred to fresh Krebs-Henseleit saline containing one of the following concentrations of ACh: (a) 10‾⁴ M; (b) 10‾⁵ M; (c) 10‾⁶ M; and (d) 10‾⁸ M. At the three top doses, immediate and powerful reabsorptions of pulmonary fluid were observed in older fetuses (60 days gestation and above); significant falls were observed in the younger fetuses. This result was unexpected, as it was hypothesized that ACh would stimulate fluid production. The threshold dose for ACh was between 10‾⁶ M and 10‾⁸ M. Phentolamine blocked the effect of ACh. This result suggested that reabsorption is a result of an indirect effect of ACh acting through pulmonary alpha receptors. The results in this study show that epinephrine, NE, AVP and ACh are all important promoters of fetal pulmonary fluid removal in the fetal guinea pig. Pulmonary alpha-adrenergic receptors mediate the effects of epinephrine, NE and ACh (indirectly). The conclusions drawn from this study emphasize the importance of species' comparison in fetal research. LIST OF ABBREVIATIONS AVP Arginine Vasopressin NE Norepinephrine DOPA dihydroxyphenylalanine PNMT Phenylethanolamine n-methyltransferase ACh Acetylcholine / Science, Faculty of / Zoology, Department of / Graduate

The generation of oxygen free radicals by the cytosolic enzyme, xanthine oxidase (XO), has been implicated in post-ischemic or reperfusion damage in several organs. XO catalyzes the conversion of hypoxanthine to urate with the concomitant production of superoxide anion free radical (0₂̅˙) and hydrogen peroxide (H₂O₂). Oxygen free radical-mediated injury has also been demonstrated in inflammatory lung disease. The possible involvement of XO in oxidative injury in the lung has not yet been studied. Therefore, this research project was designed to determine whether XO is present in the lung and to investigate its characteristics in porcine, bovine, rat and human lung and other tissues. Immunochemical analysis of xanthine oxidase in the tissues employed on polyclonal antibody raised to bovine milk XO. Proteins were separated by SDS-polyacrylamide gel electrophoresis of tissue homogenates. Proteins were transfered from the gels to nitrocellulose filters by Western blotting. After incubating the filters with a antisera containing the antibody to the purified bovine XO. XO on the filter was detected by its reaction with an enzyme-conjugated second antibody. XO was immunologically detectable in bovine lung and milk. Rat lung, kidney and liver all showed XO reactivity. XO was detectable in porcine liver but not detectable in porcine lung or kidney. Thus, the antibody to bovine XO was cross-reactive with porcine and rat XO. XO protein was not immunologically detectable in human lung possibly because the antibody was not cross reactive with the bovine antibody. In vivo, xanthine oxidase exists predominantly as a dehydrogenase rather than an oxidase. In this form as xanthine dehydrogenase (XDH) the enxyme does not produce either 0₂̅˙ or H₂O₂. The activity of both XDH and XO was measured in several tissues using a fluorometric assay which uses an artifical substrate, pterin which is catalytically converted to the fluorescent product isoxanthopterin (IXP). XO activity in porcine liver was of 1.1 x 10⁻³ µg IXP/mg protein/min although XO activity was not detectable in porcine lung and kidney, in rat lung of 1.7 x 10⁻² µg IXP/mg protein/min, rat kidney of 1.5 x 10⁻² µg IXP/mg protein/min, and rat liver of 2.2 x 10⁻² µg IXP/mg protein/min. Seven human lung biopsy samples were obtained after lung resection and initially tested for viability by determination of NADH oxidase activity and then assayed for XO-XDH. Three of these samples showed NADH oxidase activity indicating tissue viability, but only one of these three showed measurable XO activity of 5.35 x 10⁻⁶ µg IXP/mg protein/min. Irreversible conversion of XDH to XO is thought to be the result of limited proteolysis by a Ca²⁺/calmodulin activated protease, whereas reversible conversion of the enzyme occurs by oxidation of critical thiol groups. Studies on the rate and nature of fluorescence assay to detect catalytic activities of both enzyme forms. Incubation of lung homogenates with trypsin for 60 min caused irreverisble conversion of 90% of the XDH to XO. In contrast, incubation of homogenates at 15°C for 10 hours caused conversion of 100% of the XDH to XO. This conversion was reversible to the extent of 80% by reduction of thiol groups with dithiothreitol (DTT). The effects of free Ca²⁺ on the conversion of XDH to X0 was examined by using EDTA, a chelator of Ca²⁺ and other divalent cations; and EGTA, a more specific chelator of Ca²⁺. The presence of these chelating agents during homogenization of either normoxic or ischemic rat lung tissue did not inhibit reversible enzyme conversion. Increased XO activity was reversible by DTT. In the normoxic rat lung, homogenates prepared with EDTA and EGTA showed a similar conversion of 95% of XDH to XO which was reversible to 70% with DTT. In the ischemic rat lung, samples prepared with EDTA and EGTA showed a'conversion of 80% and 95% XDH to XO which was similar to control samples. The extent of reversibility to XDH was 75% with DTT incubation. In addition, perfusion of rat lungs with EDTA and DTT via a pulmonary artery cannula prior to 60 min of ischemia and homogenization did not affect the extent of XDH to XO conversion. These results indicate that irreversible Ca²⁺-mediated proteolytic conversion of XDH to XO does not occur to a great extent in the rat lung during either normoxia or ischemia. However, reversible conversion of XDH to XO does occur, suggesting that reversible thiol dependent conversion may play a role in the lung under both physiological and pathophysiological states. / Medicine, Faculty of / Pathology and Laboratory Medicine, Department of / Graduate

Lung biopsy is neither widely known nor practiced and it was only in 1949 that i first came across a paper on this subject. The title was: "Cellular analysis of the aspiration lung biopsy from normal and some pathological conditions by Z. Godlowski" (1949). The very term "lung biopsy" conjures up the picture of a needle being introduced into an air filled, very vascular structure where the bleeding of an injured vessel cannot readily be stopped, where the stage is set for air embolisms and where tension pneumothorax may occur. it was with great surprise but also an apparently innocuous procedure. Unfortunately, at that time, there was no opportunity to use the method. In 1950 I became the University Assistant at the New Somerset Hospital in Cape Town. Many of the cases admitted to the wards presented with chest pathology. Patients with pneumococcal lobar pneumonia were not infrequent and occasional cases did not resolve as expected but went on to become so-called chronic pneumonia. What happened when an acute lobar pneumonia went on to the chronic stage and why did this occur? it was suggested that investigae this problem.

Electronic Nicotine Delivery Systems (ENDS) are methods of delivering nicotine without combustion, which happens in cigarettes. These devices consist of a heating element, a battery, and a tank which stores eliquid. Over the years these devices have become more powerful, and capable of increased delivery of nicotine. There is a large variety of flavors and devices, which causes trouble for standardized studies. These devices were created to help cigarette users quit smoking; however, they are associated with significant dual use. ENDS produce lower levels of most toxic chemicals when compared to cigarettes, and significantly increased levels when compared to not smoking. Newer generation ENDS have capabilities of producing levels of reactive oxygen species and carbonyl compounds at levels similar to cigarettes. ENDS use has detrimental effects on the genome, immune system, and lung function due to exposure from these chemicals. These effects are at lower levels when compared to cigarette use. Chronic ENDS use has been associated with chronic obstructive pulmonary disorder (COPD), with an even higher association with dual use. ENDS use also causes DNA adduct formation, and activates protein kinases, nicotine acetylcholine receptors and other pathways for lung cancer as cigarette use. The full health effects of ENDS use are still unknown, from the currents studies it is clear that its use is not without harm.

Lung cancer is the most common cause of cancer-related deaths in the United States. Prevention and early detection of lung cancer are imperative in decreasing lung cancer mortality. Screening for lung cancer with low-dose computed tomography (LDCT) decreases lung cancer by 20%. Several organizations introduced lung cancer screening (LCS) guidelines in 2013, including Centers for Medicare and Medicaid (CMS) and the United States Preventive Services Task Force. However, LCS participation for eligible patients remains low, due in part to the complexity of the LCS process. The goal of this practice improvement project was to increase the knowledge of rural primary care providers regarding LCS guidelines and the related CMS requirements and to increase their confidence in initiating shared decision-making (SDM) discussions. An educational intervention consisting of a LCS educational session and a toolkit was implemented in two rural clinics. Providers at both clinics reported a benefit to the educational intervention. Pre-, immediate post-, and two-month post-education surveys were collected to evaluate the impact of the educational intervention, including provider knowledge of LCS guidelines and CMS requirements, and confidence in SDM. Project results demonstrated an increased knowledge of LCS guidelines and CMS requirements with the greatest knowledge at immediate post-education and a high level of knowledge remaining at two months post-education. A small, nonsignificant, increase in provider confidence in initiating SDM discussions occurred. At both clinics, data collected through chart audit demonstrated an improvement in documentation needed to determine LCS eligibility and increased the percentage of patients identified at high risk for lung cancer and thus, eligible for LCS. At one clinic these changes were significant. The data were further examined for SDM discussions and referrals for LDCT or to specialist for LCS with one clinic increasing SDM documentation and LDCT referrals post-education. In conclusion, although further research is needed in implementation processes of LCS, specifically in consistent documentation to improve determination of LCS eligibility of patients, this practice improvement project found education increased provider knowledge and ability to complete requirements needed to improve LDCT screenings for lung cancer.