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A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Medicine in the branch of Internal Medicine / Medical Oncology. Johannesburg 1st September 2014 / Introduction: Tyrosine kinase inhibitors and EGFR mutations has changed the treatment approach to lung cancer globally. This retrospective study will look at factors associated with EGFR mutations and define the EGFR mutation rate in South Africa. Methods: Retrospective record review from NSCLC patients in South Africa who were tested for EGFR mutations at Lancet Laboratories during 1st September 2009 to 30th June 2012. Chi-squared test was used to determine association with categorical variables. Kaplan- Meier survival analysis was done for OS and PFS between EGFR mutation positive and negative patients. Cox proportional hazards were used for subgroup analysis. Treatment practices and response were described. Results: 170 lung cancer samples were evaluable for EGFR mutation and 37 were EGFR mutation positive (21.8%). There were 22 (59.5%) exon 19 deletions, 11 (29.7%) L858R mutations, two G719X mutations, one S768I mutation and one exon 20 insertion. The median age was 63 (range 27-85). There were more females (55.6%) than males (44.4%) sent for mutation testing. Most patients were whites (71%), followed by blacks (18.3%), and other race (10.7%). 85% of all NSCLC samples tested were adenocarcinoma. None of the squamous cell carcinoma tested was positive for EGFR mutation. Smoking status was inversely proportional to EGFR mutation status (p<0.001). Over 60% patients received chemotherapy first and second line and responses decreased with each line of chemotherapy. Median PFS and OS were not different between the EGFR mutation positive and negative groups (6.85 versus 6.8 months; HR 1.6; 95% CI 0.70-3.65; p=0.2543 and 11.5 versus 12.9 months; HR 0.70; 95% CI 0.28-1.75; p=0.44, respectively). On multivariate analysis, only non-white race was associated with decrease in OS (HR 6.66; 95% CI 2.31-19.19; p=0.0004). Conclusion: EGFR mutation rate in South African lung cancer patients was 21.8%. 89% of all EGFR mutations were either exon 19 deletions or L858R point mutations. Most EGFR mutations were associated with adenocarcinoma of the lung in non-smokers. These findings were consistent with current literature in western countries. Treatment practice remained chemotherapy based, with few patients receiving EGFR TKIs. Efforts should be made to prioritized targeted treatment approach in lung cancer in South Africa.

Au travers d’études cliniques et biologiques, de méta-analyses et de revues systématiques de la littérature, nous avons étudié les CBNPC de stade III sur le plan thérapeutique et cherché des facteurs pronostiques pour la survie dans le but d’améliorer la classification internationale et, à terme, de permettre une meilleure prise en charge des patients inclus dans ce groupe hétérogène de tumeurs. Dans le cadre d’essais randomisés, nous avons montré qu’un abord multimodal et multidisciplinaire permettait d’améliorer le pronostic des patients atteints d’un CBNPC de stade III. Le traitement des tumeurs non résécables implique une combinaison de chimiothérapie et de radiothérapie, dont l’administration concomitante doit être proposée aux patients aptes à la tolérer. La chimiothérapie doit être incluse dans le schéma thérapeutique des tumeurs potentiellement résécables. Elle permet une résection chirurgicale complète chez des patients sélectionnés dont la tumeur était initialement non résécable. Nous avons déterminé que des caractéristiques cliniques (l’indice de performance et l’âge), biologiques (les taux sanguins de polynucléaires neutrophiles, d’hémoglobine et de plaquettes, la bilirubinémie) et propres à la tumeur (l’extension locale [T3-4] et ganglionnaire [N3]) avaient une valeur pronostique indépendante pour la survie. Ceci nous a permis d’aboutir à une proposition de modification de la classification internationale concernant les CBNPC de stade III. Bien que pris individuellement, les facteurs biologiques que nous avons étudiés (p53, EGF-R, TTF-1, Mdm2) n’aient pas de valeur pronostique pour la survie, nous avons montré que la combinaison EGF-R+/TTF1- était un facteur pronostique indépendant en analyse multivariée pour la survie spécifique au cancer bronchique. Nous avons finalement évalué le rôle pronostique de la tomodensitométrie par émission de positrons et de la mesure semi-quantitative de captation du 18F-FDG (SUV) sur la survie des patients atteints de CBNPC et montré qu’un SUV élevé était un facteur de mauvais pronostic pour la survie.

Energy harvesting in cellular networks is an emerging technique to enhance the sus- tainability of power-constrained wireless devices. In this thesis, I consider the co- channel deployment of a macrocell overlaid with several small cells. In our model, the small cell base stations (SBSs) harvest their energy from environment sources (e.g., solar, wind, thermal) whereas the macrocell base station (MBS) uses conven- tional power supply. Given a stochastic energy arrival process, a power control policy for the downlink transmission of both MBS and SBSs is derived such that they can obtain their own objectives on a long-term basis (e.g., maintain the target signal-to- interference-plus-noise ratio [SINR] on a given transmission channel). To this end, I propose to use two di erent forms of stochastic game for the cases when the number of SBSs is small and when it becomes very large i.e. a very dense network. Numerical results demonstrate the signi cance of the developed optimal power control policy in both cases over the conventional methods.

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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.

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.

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

Common presenting symptoms of Lung cancer are cough, hemoptysis, chest pain, dyspnea, pleurisy. Dysphagia is a very uncommon presenting feature of Lung cancer. Incidence of Dysphagia in Lung cancer is unclear from Literature. Causes of Dysphagia in case of Lung cancer are Anatomically classified as Oropharyngeal and Esophageal. Causes of oropharyngeal dysphagia are oral candidiasis, oropharyngeal Metastasis of Lung cancer. Causes of esophageal dysphagia are Cervical or Mediastinal Lymphadenopathy, Motor dysfunction because of Brain stem Metastasis, Lambert eaton syndrome, Esophageal candidiasis, Radiation esophagitis. Here by we present an Unusual presentation of an aggressive disease, poorly differentiated SCLC presenting as Mid esophageal dysphagia secondary to extrinsic esophageal compression. 65 year old female with past medical history of Diabetes, Hypertension presented with complaints of worsening sub sternal chest pain radiating to back since last 2 days and progressive dysphagia. Pt underwent Left heart catheterization revealing non obstructive coronary artery disease. Modified Barium swallow showed stasis of contrast in mid esophagus, Endoscopy showed extrinsic compression of the proximal esophagus, normal mucosa. Computerized tomography of chest was done for further evaluation, revealing extensive left cervical, mediastinal, left hilar lymphadenopathy causing extrinsic compression of the esophagus and encasement of the left hilar structures. Further evaluation through Bronchoscopic biopsy of her left upper lobe mass reveals poorly differentiated small cell carcinoma. Staging was performed revealing limited stage disease. Started on concurrent chemotherapy with cisplatin, etoposide and radiation. As SCLC is highly responsive to chemotherapy and radiotherapy sensitive patient got symptomatic relief by the end of first cycle. SCLC is an aggressive lung cancer. As it is a micro metastatic disease in nature at presentation, it’s management is entirely different from Non SCLC. SCLC being an aggressive disease can cause dysphagia in 1-2% during the disease course. SCLC presenting as dysphagia is almost never reported in the literature. Our patient presented with severe dysphagia, described it as “a tennis ball sitting in her food pipe”. Fortunately she presented to the Emergency room with dysphagia and associated chest pain, we were able to make early diagnosis of SCLC, initiate treatment. Delay in the diagnosis lead to rapid progression of disease and poor prognosis. Through our case we wanted to convey that it is very important to obtain meticulous history, keeping broad differentials, which can help improve prognosis. Because not always the presenting features are from the organ of involvement it could be from the contiguous spread or compression.

Vaults, recently discovered in 1986, are multi-subunit organelles with a molecular mass of ,--,13 MDa. The specific function of vaults is unknown, although they are believed to be involved in internal transport. These ribonucleoproteins are composed of the major vault protein, which comprises ' 70% of the vault's mass, two minor proteins, TEP1 and vPARP, and untranslated RNA(s). It is believed that the protein components of the vault are structural while the RNAs are the functional components. Implications of the vault's involvement in multi-drug resistance in cancer have been made. In some resistant cancer cells, the major vault protein and vRNA(s) are up-regulated up to 15 times when cells are exposed to a cytotoxic drug. Cytotoxic drugs such as doxorubicin are administered as a cancer treatment, but may be ineffective because the drug is actively pumped out of the cell. Multi-drug resistance is the most common failure of chemotherapeutic cancer treatment. In order to prevent the development of multi-drug resistance this research employed the use of small interfering RNA technology to down-regulate the expression of one of the vault RNAs, vRNA3, in cultured GLC4 cells, a small-cell lung cancer cell line. If the vRNA(s) are the functional portion of the vault and a cloned siRNA prevents their up-regulation after drug exposure, the cells should lose their multi-drug resistance, stimulating apoptosis. If successful, this approach may provide an alternative approach to cancer treatment in cells which respond to chemotherapy by increasing the number of vault particles.Initially, the transfection of a plasmid into GLC4 cells was optimized. The best transfection efficiency (N20%) was obtained by using GeneTherapySystems' GenePORTER2 transfection reagent in serum free conditions. To determine if the vault RNAs are the functional portion of the vault complex that confers multi-drug resistance to a cell, a small interfering RNA fragment was designed to specifically knock-down the expression of human vault RNA 3. The siRNA sequence homologous to a portion of vault RNA3 was cloned into an expression vector, and using optimized transfection protocols was transfected into GLC4/REV cells. A Western analysis using caspase-8 antibodies showed no difference in caspase-8 expression in doxorubicin treated and untreated cells. Preliminary results yielded by reverse transcriptase polymerase chain reaction amplification of isolated RNA indicated that the vRNAs were not down-regulated by the siRNAs. / Department of Biology