Some suburbs within North West (NW) metropolitan Adelaide have lung cancer mortality up to twice that expected from state averages. Previous international research investigating high lung cancer rates in similar shared industrial and residential areas have had inconsistent results. This case control study was conducted to determine whether residential exposure to industry is a risk factor for lung cancer in NW Adelaide. Contemporary ambient air monitoring was undertaken as an indicator of future respiratory health risk. 142 lung cancer patients and 415 age, gender matched population controls were interviewed utilising an event history calendar. Lifetime exposure indices were calculated for cigarette smoking, passive smoking, occupation, air pollution (residential proximity to industry) and hobbies. Data was analysed utilising chi- quared and conditional logistic regression. Ambient carcinogens and fine particulates with potential industrial sources in the region were monitored in five locations. In the final multivariate model leaving school early, pack- years of cigarettes and not living in close proximity to the power station or light industrial area were statistically significant risk factors for lung cancer. A composite score of residential exposure to all industries was not significant. However cautious interpretation is required as it was noted participating controls resided significantly closer to industry than non-participants. Average concentrations of ambient carcinogens were within guidelines; however diesel exhaust particulate and Polycyclic Aromatic Hydrocarbons were elevated at sites in proximity to heavy vehicle traffic. Diurnal variations in PM[subscript 2.5] included weather and traffic-related short term peaks, and other peaks potentially related to industrial activity. Cigarette smoking is likely to be the primary cause of elevated lung cancer mortality in suburbs of NW Adelaide. The negative effect of residential exposure to two industries may be due to participation bias. Whilst having more thorough exposure assessment than previous research, this study may have been limited by low participation rates in cases and controls. Air monitoring data suggests there is not a significant public health risk at present; however these results are unlikely to be indicative of historical exposures. Future public health initiatives to curb high lung cancer mortality in the NW should focus on smoking prevention and reduction strategies. / Thesis (Ph.D.)--Department of Medicine and Department of Public Health, 2004.

Where is the Person in Symptom Cluster Research? The Experience of Symptom Clusters in Patients with Advanced Lung Cancer This thesis describes a three-year qualitative study which aimed to explore the experience of symptom clusters in patients with advanced lung cancer. The study employed a patient-focused approach utilising Interpretative Phenomenological Analysis (IPA) (Smith et al. 2009a). This methodology (IPA), informed by a contextual constructionist stance, was selected to explore the experience of symptom clusters, for its focus on the lived experience, the context and meanings which surround such experiences and its idiographic approach. Ten patients (a sample size which is the upper limit of the number of participants advocated for studies employing IPA (Smith et al. 2009b;Reid et al. 2005;Smith and Osborn 2004)) with advanced lung cancer took part in the study and data were collected using unstructured, in-depth interviews at two time points: on recruitment and three to five weeks later. Data were analysed using Interpretative Phenomenological Analysis, within the framework advocated by Smith and Osborn (2003). The study generated interesting and significant findings. The experience of symptom clusters in patients with advanced lung cancer was characterised by two super-ordinate themes: ‘The lived experience of symptom clusters and the role of context and meaning’ and ‘Symptom clusters and loss of sense of self’. The super-ordinate theme of ‘The lived experience of symptom clusters and the role of context and meaning’ in the first instance, illustrates that the participants in this study were experiencing symptom clusters and providing detail on the components, nature and patterning of the symptom clusters reported, particularly the way that one or two salient symptoms were commonly highlighted from all the other symptoms experienced. This super-ordinate theme also demonstrates the core role that context and meaning play in the lived experience of symptom clusters, with many of the participants in this study framing their experiences of symptom clusters within a fear of death, stigma and loss of sense of self. The second super-ordinate theme informing this thesis is ‘Symptom clusters and loss of sense of self’. This super-ordinate theme illustrates the impact of symptom clusters on the participants’ lives, and how this, in turn, impacted on their sense of self in a number of different ways. For some, their sense of self was compromised by the concurrent symptoms that they were experiencing, as they prevented them from undertaking roles and activities that they were accustomed to in the past. This super-ordinate theme also highlights the role of the body relative to the self, and describes how the participants’ sense of self was transiently lost during periods when they experienced symptom clusters of high severity. The findings presented also demonstrate the knock-on effect of loss of sense of self experienced, with the participants feeling like they were a burden due to their incapacitation, and at times hiding the multiple symptoms that they were experiencing, in a bid to protect their loved ones from their illness. In light of the loss of sense of self experienced, this super-ordinate theme also demonstrates how the participants employed various strategies in a bid to try and maintain a coherent and valued sense of self. The findings presented illustrate how the use of IPA facilitated the collection of data that provided an in-depth understanding of the complexity of the experience of symptom clusters in patients with advanced lung cancer, adding a unique contribution to this body of knowledge. The results of this study highlight the limitations of definitions that currently underpin the study of symptom clusters in patients with cancer and the current empirical base to date, particularly the way that they do not acknowledge the core role that context and meaning play in the lived experience of this phenomenon. This lack of recognition of these core elements of the patient experience of symptom clusters poses the risk of this body of research producing data that have limited relevance to the patient and therefore clinical practice. It is therefore proposed that the study of symptom clusters in patients with cancer needs to move away from the reductionist approach which currently dominates and to broaden its scope, to one that acknowledges the complexity of the experience of symptom clusters, the core role that context and meaning play in such experiences, and contributions that patient experience can make in advancing this important and emerging body of research.

Theoretical studies focusing on the nature of landscapes that correlate molecular sequences to molecular function have mainly been carried out in silico due to the vast amounts of data that are needed for analysis. In vitro selections of aptamers are a good model system to study theoretical questions at a experimental level. With the introduction of robotic platforms that conduct in vitro selections, it is now capable of producing significant amounts of data in a short time, making theoretical modeling with real experimental data attainable. I will be using a Biomek 2000 Laboratory Automation Workstation to carry out multiple in vitro nucleic acid selections in parallel. I will explore the sequence space to examine whether existing in vitro selection systems are optimal at isolating the best winning species. New methods will be introduced that will allow for the selection of identical targets with identical pools free of cross contamination on the open robotic system. This will open the doors to further conduct selections against other identical or highly similar targets, such as complex cellular targets. Finally, I will investigate the methods to improve the effectiveness at isolating aptamers against the highly complex lung cancer cell lines. These targets are highly challenging for isolating specific aptamers because of the great diversity of biomarkers found among them. Moreover, their highly morphological similarity of the cultured cells makes selections for specific aptamers very difficult. I explore the different methods that will allow for the generation of aptamers that can distinguish between non-small cell lung cancer and small cell lung cancer, and between non-small cell lung cancer and normal lung cells. Fine-tuning of this process is essential at transferring this process to automated platforms for large-scale generation of biosensors against tumor biomarkers.

published_or_final_version / Pathology / Master / Master of Philosophy

The loss of muscle mass leading to cachexia is rarely identified in early lung cancer. Fasting blood and muscle biopsy were collected in 59 non-small cell lung cancer (NSCLC) and 16 non-cancer patients, at the beginning of thoracic surgery. Serum C-reactive protein (CRP), and IL-6 were higher in NSCLC. In weight-losing NSCLC, food intake and serum albumin were lower, CRP, and TNF-alpha were higher. Although the expression of genes of the ubiquitin-proteasome system was not different, ubiquitinated-protein levels were lower and negatively correlated with ph-FOX01 in weight-losing patients. This would suggest lower muscle proteolytic rates in the early stages of NSCLC. Ph-FOXO1 also related to the degree of weight loss and stage of NSCLC. These data suggest that in early stages of the disease, weight and muscle loss could be mainly due to reduced food intake, rather than accelerated proteolysis, which reinforces the potential for successful dietary interventions to prevent or delay the onset of cachexia.

Lung cancer is the most common cancer worldwide and is the fourth leading cause of death in South Africa. Lung cancer is categorised into two types; non-small cell lung cancer and small cell lung cancer (SCLC). SCLC constitutes 20% of all lung cancers and is considered to be an aggressive tumour as it gains chemo-resistance and exhibits early metastasis in diagnosed patients. SCLC cells originate from the neuroendocrine cells of the bronchoepithelium and are known to secrete the neuropeptide, proopiomelanocortin (POMC). POMC undergoes proteolytic cleavage to produce the adrenocorticotropin hormone (ACTH). ACTH stimulates the production of the steroid hormone, glucocorticoid hormone (GC), through the hypothalamus-pituitary-adrenal (HPA) axis. The produced GCs mediate a negative feedback system of the HPA axis to sequester ACTH production. SCLC cells are insensitive to this negative feedback stimulus. GCs elicit their actions through the glucocorticoid receptor (GR). Studies have shown that SCLC cells have a reduced expression of GR which perpetuates the GC-insensitivity. Importantly, over-expression of exogenous GR in SCLC cells leads to cell death by apoptosis. It was postulated that SCLC cells select against GR expression for longevity. Cancer cells are known to alter/silence the expression of tumour suppressor genes by a mechanism known as methylation. Methylation occurs when the enzyme, DNA methyltransferase 1, adds a methyl group to a cytosine present in a guanine-cytosine rich region of the gene (CpG island). The GR gene has a 5’-untranslated exon 1 region that consists of eight promoter regions (1A-1J), in these promoter regions are many CpG islands that have the potential to be methylated. The first aim of this study was to determine the promoter/s utilised by SCLC cells to express the GR protein. Conventional PCR revealed that all three cell lines predominantly utilise promoters 1B and 1C for GR expression. Bioinformatic analysis revealed that these promoters contain putative CpG islands and new data suggests that the GR is silenced by methylation and that treatment with a de-methylating agent results in GR re-expression. To determine which promoter is responsible for GR re-expression after de-methylation, the SCLC cell line, DMS79, as well as two control cell lines, A549 and HEK cells, were treated with the de-methylating agent, 5-aza-2’-deoxycytidine, for 72 hours. qPCR analyses revealed that all three cell lines expressed promoters 1B and 1C with A549 cells showing no evidence of methylation. The HEK cells showed methylation in promoter 1C and not promoter 1B. The SCLC cells showed methylation in both promoter 1B and 1C, however, only promoter 1B showed a significantincrease in transcript levels. SCLC cells are induced to undergo GC-mediated apoptosis when GR expression is restored however the mechanism utilised by the GR to induce the apoptotic cascade is unknown. The GR structure is divided into three domains; ligand binding domain (LBD), DNA binding domain (DBD) and amino terminal domain (NTD). The second aim of this study was to determine the component of the GR that induces apoptosis of SCLC cells. HEK and SCLC cells were infected with empty virus and various GR construct viruses; containing either a wild-type GR, ligand binding mutant, DNA binding mutant or a transactivation mutant (NTD); for 72 hours. Both cell lines were quantified for apoptosis and cell death using microscopic analyses. In HEK cells, it was shown that apoptosis occurred in cells expressing the wild-type GR, the DNA binding mutant and transactivation mutant constructs but apoptosis was reduced in cells expressing the ligand binding viruses. This indicates that the LBD may be necessary for inducing apoptosis in HEK cells. In DMS79 cells, apoptosis occurred in cells expressing the wild-type GR, ligand binding mutant and the DNA binding mutant constructs. There was less apoptotic activity exhibited in the transactivation constructs which indicates the NTD may be necessary for apoptosis induction in these cells. The NTD of the GR is responsible for interaction with other transcription factors to mediate GR transcriptional activity and this study has shown that the transactivation domain plays a necessary role in apoptosis induction. An analysis of the various pathways the GR interacts with through the NTD domain could lead to the identification of the pathway which triggers apoptosis in SCLC cells. This discovery, together with knowledge of promoter methylation and expression may contribute to the development of new, more effective therapies for SCLC. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

The goal of conformal radiation techniques is to improve local tumour control through dose escalation to target volumes while at the same time sparing surrounding healthy tissue. Respiratory motion is known to be the largest intra-fractional organ motion and the most significant source of uncertainty in treatment planning for chest lesions. A method to account for the effects of respiratory motion is to use four-dimensional radiotherapy. While analytical models are useful, it is essential that the motion problem in radiotherapy is addressed by both modeling as well as experimentally studies so that different obstacles can be overcome before clinical implementation of a motion compensation method. Validation of techniques aimed at measuring and minimizing the effects of respiratory motion require a realistic dynamic deformable phantom for use as a gold standard. In this work we present the design, construction, performance and deformable image registration of a novel breathing, tissue equivalent phantom with a deformable lung that can reproducibly emulate 3D non-isotropic lung deformations according to any real lung-like breathing pattern. The phantom consists of a Lucite cylinder filled with water containing a latex balloon stuffed with dampened natural sponges. The balloon is attached to a piston that mimics the human diaphragm. Nylon wires and Lucite beads, emulating vascular and bronchial bifurcations, were glued at various locations, uniformly throughout the sponges. The phantom is capable of simulating programmed irregular breathing patterns with varying periods and amplitudes. A deformable, tissue equivalent tumour, suitable for holding radiochromic film for dose measurements was embedded in the sponge. Experiments for 3D motion assessment, motion reproducibility as well as deformable image registration and validation are presented using the deformable phantom.

Thesis (M.Sc. (Biochemistry)) -- University of Limpopo, 2020 / Despite major advancements in the development of various chemotherapuetic agents, treatment for lung cancer remains costly, ineffective, toxic to neighbouring normal noncancerous cells and still hampered by high level of remissions (Wistuba et al., 2018; Tana et al., 2016; Schiller et al., 2002). Synthesis of novel quinoxalines with a wide spectrum of biological activities has recently received considerable attention with promising anticancer drug activity since most of them do not affect non-cancerous cells and are derived from readily available less costly raw materials (Srivastava et al., 2014). Since combination treatment has been shown to augment and improve single drug treatment, trace elements were employed in this study in combination with quinoxalines derivatives (Gomez et al., 2016; Kocdor et al., 2015; Ku et al., 2012; John et al., 2010; Killile and Killilea, 2007). Zinc is an essential element that is integral to many proteins and transcription factors which regulate key cellular functions such as the response to oxidative stress, DNA replication, DNA damage repair, cell cycle progression, and apoptosis (Dhawan and Chadha, 2010). Owing to the importance of these two approaches, the aim of this study was to provide in vitro preliminary anticancer activity data on A549 lung cancer cells using combination of zinc and quinoxaline derivatives. An assessment of the quinoxaline derivatives ferric reducing power and DPPH free radical scavenging activity was performed. The cytotoxic and anti-proliferation activity of these derivatives and zinc on cancer cell lines was determined using the MTT assay. The ability of the quinoxaline derivatives and zinc to modulate oxidative stress was evaluated using the H2DCFDA fluorescence assay. Cell cycle arrest stages were analysed by flow cytometry through propidium iodide cell cycle analyses. The ability of the quinoxaline derivatives to induce apoptosis in cancer cells was assessed using DAPI/PI, Acridine Orange/Ethidium Bromide (AO/EB) and Annexin V-FITC/Dead Cell assays. Western blot was used to investigate the Bcl/Bax expression ratios in A549 lung cancer cells after treatment with quinoxaline derivatives, zinc and in combination. Of the four quinoxaline derivatives tested, 3-(quinoxaline-3-yl) prop-2-ynyl methanosulphate (LA-39B) and 3-(quinoxaline-3-yl) prop-2-yn-1-ol (LA-55) produced significant anticancer properties against A549 lung cancer cells at minimal concentrations of 25μM. Both quinoxaline derivatives displayed antioxidant properties and did not induce cell death in non-cancerous Raw 267.4 macrophage cells. Cytotoxicity was observed in A549 lung cancer, HeLa cervical cancer and MCF-7 breast cancer cells albeit inhibition was more pronounced in A549 lung cancer cells. Treatment of cancer cells with zinc also resulted in pronounced cytotoxicity at a minimal concentration of 25μM. Although reduced oxidative stress was observed in Raw 264.7 macrophages, in A549 lung cancer cells both compounds were able to increase ROS production which was accompanied by high levels of apoptosis when treated with derivatives and zinc alone but when in combination an improved higher level of apoptosis is observed. The improved anti-cancer activity of this drug combination treatment was further accompanied by lower Bcl/Bax expression ratios with upregulation of Bax in A549 lung cancer cells. The results of the study suggest that 3-(quinoxaline-3-yl) prop-2-ynyl methanosulphate and 3-(quinoxaline-3-yl) prop- 2-yn-1-ol are potential candidates drug for treatment of lung cancer. The use of these quinoxaline derivatives in combination with zinc can offer alternative treatment options for lung cancer. / National Research Foundation (NRF)

Purpose: In the contemporary management of early-stage lung cancer with RadiationTherapy (RT), there is increased imaging utilization for the diagnosis and treatment and follow-up after completion of treatment. We evaluated whether this increased radiation exposure to patients with early-stage lung cancer that receive stereotactic body radiotherapy (SBRT) significantly increases the risk of radiation-induced carcinogenesis (RIC). Methods: Following IRB approval, one hundred and ninety-six consecutively treated lung cancer patients treated with SBRT were selected for analysis. Information collected included demographics and all ionizing imaging scans one year before SBRT treatment and one year following treatment. These included chest X-rays (CXR), computerized tomography scan (CT scan), positron emission tomography scan (PET-CT scan), bone scan, ventilation-perfusion scan (VQ scan), cone-beam CT scans. In addition to the lung cancer patients, comparative data on ten prostate and breast cancer patients each was collected to get an estimate of the radiation-induced risk (RIC) in other common malignancies. For each patient, the total effective dose (mSv) was calculated by the sum of all effective doses for all scans (1 year before SBRT to 1-year post-SBRT). After calculating the total effective dose, the summed dose was used to calculate the RIC using the RadRat tool. For the study, we decided that a 1% increase in the baseline risk of radiation-induced lung cancer will be considered a significant increase. Results: Among lung cancer patients, there were 87 males (44.4%) and 109 females (55.6%). The median number of Pre-SBRT CXRs (PA/lateral) was 2 (Range: 1-22), the median number of pre-SBRT CT scans was 2 (Range: 1-6), the median number of pre-SBRT PET-CT scans was 1 (Range: 1-4), the median number of Bone Scans or VQ scans pre-SBRT was 1. The median effective exposure dose from all scans was 72mSv (Range: 24-140.36mSv). The median excess lifetime risk (ELR) of developing lung cancer (a chance in 100,000) with a 90% uncertainty range was 57.15. The Excess Future risk (EFR), the risk from 2019 to the end of the expected lifetime of developing cancer (a chance in 100,000), showed a median of EFR mean of 73.75 (Range: 8.45- 416). The total future risk (TFR, a sum of baseline and excess risk) of developing cancer, from 2019 to end of an expected lifetime was 2732.5 (Range: 808-8290), the median of TFR upper bound was 2785.5 (Range: 856-8400) and median of TFR lower bound was 2679.5 (Range: 761- 8183). At 6 months, survival was 94.7% (144/152), at 1 year, 79% (94/119), at 3 years 32.5% (27/83). At five years, with survival data on 77 patients available, 9 (11.6%) were alive. Regarding the comparison of RIC from imaging before RT for patients with prostate cancer, the median total effective radiation dose from all pre-SBRT and post-SBRT scans was 20mSv (Range: 20-30mSv), and the median of mean ELR for development of RIC prostate cancer was 4.24 (per 100,000). Regarding early-stage breast cancer, the median total effective radiation dose from all pre-RT and post-RT scans was 16.56mSv (Range: 10.52-31.48mSv), and the median of mean ELR for development of RIC was 35.95 (per 100,000). Conclusion: The median excess cancer lifetime radiation-induced cancer risk for the lung cancer cohort was 0.05%, which is significantly less than the 1% risk that was determined to be clinically significant as per our study objective. The survival in this cohort of patients was poor. Enhanced imaging to enhance staging accuracy, safety during SBRT treatment, and adequate follow-up outweigh the RIC risk.

Thesis (M.Sc. (Biochemistry)) -- University of Limpopo, 2021 / Lung cancer is the most diagnosed cancer with an estimated 3 million deaths expected by 2035. Bioactive phytochemicals present in plants are preferred as anticancer therapeutic agents, due to their ability to differentiate between cancerous and normal cells. One such plant, Senna italica, is traditionally used to treat diabetes, malaria, constipation, jaundice, fever and sexually transmitted diseases. Several studies have reported on its anti-proliferative potential against different types of cancers. However, there is scanty information regarding its molecular mechanism of action against different types of cancers, more especially lung cancer. This study, therefore, aims to determine the differential expression profiles of apoptotic genes in lung A549 cancer cells induced by treatment with S. italica leaf and root extracts in an attempt to understand its purported anticancer molecular mechanism of action. The leaves and roots of S. italica were dried in the dark and extracted with ethyl acetate and methanol. Screening for the presence of secondary metabolites was performed using thin layer chromatography and various standard chemical-based tests. The total phenolic and flavonoid compounds were evaluated using gallic acid and quercetin equivalence assays. The antioxidant activity of S. italica extracts was determined using DPPH free radical scavenging and ferric ion reducing power assays. The cytotoxicity of both leaf and root extracts on lung A549 cancer cells was evaluated using 3-(4,5- dimethylthiazol-2-yl)-2-5-diphenyl tetrazolium bromide (MTT) and further confirmed by Muse cell count and cell viability assays. The proliferation of cells, after treatment with different concentrations of the extracts, was examined using the Ki67 proliferation assay. Genotoxicity was determined to assess the potential damage caused by the extracts on the DNA using a MUSETM multicolour DNA damage kit following manufacturer’s protocol. The morphological change of cells treated with different concentrations of S. italica ethyl acetate root extract was analysed using acridine orange/ ethidium bromide (AO/EB) dual staining assay and examined under fluorescent light. The total number of cells undergoing apoptosis was also determined using the Annexin V assay. The expression of 84 key genes, involved in programmed cell death or apoptosis, was determined using the Human Apoptosis RT² Profiler PCR array kit. Senna italica methanol extract had a high content of plant materials in both leaves and roots compared to the ethyl acetate extract. A higher phenolic content was observedxii mainly in the leaf extract and a higher flavonoid content was observed in the root extract. Phytochemicals, such as phenols, tannins, flavonoids, terpenoids and steroids, which are known to exhibit anti-cancer activity against cancerous cells were abundant in the ethyl acetate leaf and root extracts as compared to the methanol leaf and root extracts. Additionally, the ethyl acetate root extract exhibited more antioxidants and radical scavenging activity in comparison to the methanol root extract. The IC50 of ethyl acetate root extract was determined to be 200µg/ml. Both methanol and ethyl acetate root extracts had little to no effect on the viability of lung A549 lung cancer cells. The results were confirmed by cell count and viability assay results. The cytotoxicity of ethyl acetate root extract was also evaluated against the normal kidney HEK-293 cells, which displayed little cytotoxic effect. The proliferation results indicated that S. italica ethyl acetate root extract has the potential to reduce the proliferation of lung A549 cancer cells. The ethyl acetate root extract was found to induce late apoptosis in A549 cells, but the genotoxicity data indicated that the DNA double strand breaks (DSBs) were repairable. The results further showed an expression of different genes that inhibit apoptosis, such as XIAP in lung A549 cells, following treatment with S. italica ethyl acetate root extract. In conclusion, the ethyl acetate root extract displayed a promising anti-cancer therapeutic potential, and thus warrants further investigation to elucidate the identity of the inherent chemical components that are responsible for the observed biological activity. / University of Limpopo and SAMRC