Dissertations / Theses on the topic 'Cancer aetiology'

This work stems from the discovery that certain sexually transmitted types of human papillomavirus (HPV) are the main causal agents in cervical carcinogenesis. The thesis sets out to explore the psychosocial issues that arise from linking a sexually transmitted infection with cervical cancer. Four studies were carried out. Study 1 was a survey of women attending a well-woman clinic (n=1032) and assessed awareness and knowledge about HPV. Study 2 used a population representative sample of men and women (n=1937) to assess beliefs about the risk factors for cervical cancer. Study 3 used in-depth interviews to explore the beliefs and experiences of 74 women who had taken part in HPV testing. Study 4 was a continuation of Study 3, in which 30 women were interviewed following participation in their second HPV test, a year after the first. Awareness of HPV and its link with cervical cancer was found to be low. Although there was higher awareness of sexual activity as a risk factor for cervical cancer, this was far from universal. Women testing positive for HPV who understood that it was sexually transmitted frequently reported negative emotional and social responses, different from those that have been found among women with abnormal smear test results. Leventhal's Common Sense Model of self-regulation in health and illness provided a useful framework within which to conceptualise the relationship between women's cognitive representations of HPV and their responses to the infection. It seemed that women were also engaged in the self-regulation of their relationships and were motivated to develop representations of HPV that did not impugn their current partners. Diagnosis with persistent HPV infection was associated with higher levels of anxiety about health and with the desire for immediate further investigation by colposcopy, rather than continued surveillance. The introduction of HPV testing and vaccination should be accompanied by widespread public education. If information provision is not handled in a sensitive way, it could cause confusion and stigmatise cervical cancer. More research is needed to develop ways to communicate information about HPV effectively.

Breast cancer is the most common cancer in women and is also the leading cause of cancer mortality in women. There are several known risk factors for breast cancer including genetic factors which account for at least 25% of the incidence of breast cancer, although only a small proportion of this is a result of mutations in known high penetrance susceptibility genes. The majority of genetic risk is now thought to be due to common genetic variants, for example single nucleotide polymorphisms (SNPs). We investigated whether SNPs in candidate genes, with a biological reason for being of interest to study in relation to breast cancer, were correlated with the development of tumours with a certain phenotype, such as grade, lymph node involvement, oestrogen receptor status and the presence of distant metastases. We genotyped 206 SNPs across 30 candidate genes in 1001 patients. Association was performed using Cochran-Armitage trend test and 2-by-3 tables of disease by genotype. We replicated observations from previous studies such as the association of SNPs in FGFR2, TNRC9 and ATM with oestrogen receptor status and identified novel associations of SNPs in the oestrogen receptor gene and matrix metalloproteinase-9 gene (MMP-9) with grade and presence of distant metastasis respectively. The function of two promoter SNPs in MMP-9 were further investigated using luciferase reporter gene assays. The C allele of rs3918242 had a 1.5 fold increase in MMP-9 expression in MDA-MB- 231 cells and the A allele of rs3918241 showed a slight increase in MMP-9 expression in MCF-7 and NIH-3T3 cell lines although not significant. The novel results identified need to be replicated for validation but this study provides evidence that common genetic variants play a role in predisposing to certain tumour types.

Oesophageal adenocarcinoma (OAC), a cancer with dismal prognosis, has been increasing rapidly in incidence over the last 30 years, nowhere more so than in the UK. Intriguingly, it is a disease predominantly among white males, but there is a paucity of data from England. In performing a range of epidemiological studies, it has been confirmed that OAC has risen five-fold in the West Midlands, UK, five times more common among men, and predominantly a disease among Caucasians. A reduced incidence of OAC was identified among subjects with prostate cancer, suggesting a protective effect of anti-androgen therapy. Examination of a general practice database revealed a negative association with aspirin, non-steroidal anti-inflammatories and statins with OAC, and a positive association with inhaled steroids, increasing number of drugs with a side effect of reducing the lower oesophageal sphincter, and drugs used for asthma/COPD. Finally, a region wide case-control study, confirmed the positive association seen with increasing body mass index, waist circumference, smoking and reflux symptoms, with negative associations seen with a diet high in fruit and vegetables. This work has identified potentially modifiable risk factors that may be employed to reduce the incidence of oesophageal adenocarcinoma, and better help stratify those most likely to benefit from endoscopic surveillance.

Prostate cancer is the most common cancer among Swedish men, but the aetiology of this disease is largely unknown. There is evidence for a linkage between chronic inflammation and prostate cancer. The mechanisms causing prostate inflammation and how this could promote tumour development and progression are however largely unknown. Chronic inflammatory infiltrates are common findings in prostate tissue samples and infection is proposed to be one possible cause for this inflammation. Inflammatory cells release free radicals, cytokines, and growth factors that facilitate increased cell proliferation, DNA damage, mutations, and angiogenesis. However, the present literature on the presence of microbes in prostate tissue and their possible linkage to inflammation and cancer development is limited. Therefore, the aim of this thesis was to investigate if microorganisms are present in prostate tissue and to evaluate their role in inducing prostatitis and prostate epithelial neoplasia. The presence of microorganisms (virus, bacteria and fungi) was studied in clinical prostate tissue samples to evaluate whether or not the occurrences of microorganisms were different in patients that later developed cancer compared with matched controls that did not. Viruses, bacteria and fungi were found in prostate tissues. Out of eight different viruses investigated, EBV and JC virus were detected, but there were no differences in occurrence in the case group compared to the control group. The fungus Candida albicans was present in a very small proportion of the prostate tissue samples. The predominant bacterium was Propionibacterium acnes and the second most prevalent was Escherichia coli. The presence of Propionibacterium acnes was associated with inflammation and subsequent prostate cancer development. Propionibacterium acnes was further evaluated for its capacity to induce an inflammatory response both in vitro and in vivo. Live Propionibacterium acnes induced a strong immune reaction in prostate epithelial cells in vitro with up-regulation of inflammatory genes and secretion of pro-inflammatory cytokines. Infection with Propionibacterium acnes in rat prostate resulted in a lobe specific inflammation with the most intense inflammation in the dorso-lateral prostate, lasting up to 3 months post-inoculation. Propionibacterium acnes inflammation was also associated with altered epithelial cell morphology, signs of DNA damage and increased cell proliferation. Taken together, this thesis shows that different viruses and bacteria can be found in prostate tissue. Propionibacterium acnes, the most abundant among the bacteria detected and more prevalent in the cancer than in the control group, exhibits strong prostatitis promoting properties both in vitro and in vivo. In addition, Propionibacterium acnes can induce some of the epithelial changes known to occur during prostate neoplasia formation. This thesis therefore suggests that Propionibacterium acnes induced chronic prostatitis could promote prostate cancer development. Further studies are needed to elucidate the molecular interplay linking Propionibacterium acnes induced inflammation and the formation of a pre-neoplastic state that could evolve into prostate cancer.

Les cellules cancéreuses sont caractérisées par des altérations de l'ADN causées par des facteurs exogènes, comme l'exposition à des agents environnementaux tels que le tabac ou les UV, ou par des mécanismes endogènes tels que les erreurs de polymérase lors de la réplication de l'ADN. L'analyse des causes et des conséquences de ces altérations permet de mieux comprendre les facteurs et mécanismes à l'origine du développement d'un cancer. Les technologies de séquençages à haut débit offrent l'opportunité d'étudier la nature précise de ces altérations à l'échelle du génome et permettent de révéler des signatures mutationnelles distinctes et spécifiques de cancérigènes, fournissant ainsi des hypothèses sur l'étiologie des cancers.L'objectif de ma thèse a consisté à développer des méthodes et des outils bioinformatiques accessibles et conviviaux permettant de faciliter l'analyse et l'interprétation des signatures mutationnelles à partir de données de séquençage à haut débit. L'application de ces outils et méthodes à des séries originales de tumeurs humaines et de systèmes expérimentaux de mutagénèse et carcinogénèse a permis de mieux caractériser la signature mutationnelle de l'acide aristolochique (AA) ainsi que d'autres cancérigènes d'intérêt
Cellular genomes accumulate alterations following exposures to exogenous factors, like environmental agents such as tobacco smoking or UV, or to endogenous mechanisms such as DNA replication errors. Analysing the causes and consequences of these changes allows a better understanding of the mechanisms underlying cancer development and progression. Next-generation sequencing (NGS) technologies provide the opportunity tostudy the nature of the resulting alterations on a genome-wide scale and started to reveal distinct mutational signatures specific to past carcinogenic exposures providing clues on cancer aetiology.The aim of my thesis was to develop user-friendly bioinformatic tools and methods for facilitating the analysis and interpretation of carcinogen-specific mutational signatures from NGS data. Applying these tools and methods to human tumours and experimental models of mutagenesis led to a better characterisation the mutational signature of aristolochic acid (AA), as well as other carcinogens of interest

Prostate carcinoma represents one of the leading causes of cancer death in men within the Western world, Several studies have hypothesised that chronic prostatic inflammation may predispose men to developing this malignancy. In 2005, the Gram-positive anaerobe, Propionibacterium acnes was identified as the predominant bacterium in cancerous prostate glands; with its pro-inflammatory nature illustrated following acute and chronic infection of such cells both in vitro and in vivo, The main objective of this study was therefore to further elucidate the potential role of p, acnes in the aetiology of prostate cancer. Firstly, the inflammatory response of normal prostate epithelial cells (RWPE-1s), following short-term exposure to a number of P. acnes phylogroups, was examined; with particular interest on the effects of infection on expression of pro-inflammatory molecules, such as PAR-2. Next, long-term infection studies Were performed to evaluate P. acnes persistence, and the mechanisms by which this bacterium stimulates chronic prostatic inflammation. Short-term P. acnes infection potently induced PAR-2 expression in RWPE-1s, as revealed by RT-PCR and Western! immunoblotling; with all strains also found to enhance secretion of inflammatory mediators, including IL-6 and IL-8. Distinct phylotypic differences were noted during these studies; thus underpinning reports of diversity among P. acnes phylotypes. Total viable counts demonstrated the ability of P. acnes to establish chronic RWPE-1 infection; thereby facilitating the induction of sustained prostatic inflammation, achieved through augmentation of PAR-2, and increased release of pro-inflammatory molecules, Moreover, qRT-PCR array analysis revealed P. acnes infection to upregulate many pro-angiogenic genes; a response reflected during in vitro tubule assays upon incubation of HMEC-1 s with conditioned media obtained from P. acnes-infected RWPE-1s. Taken together, the findings obtained these studies highlight prostatic P. acnes infection as a potential risk factor for prostate carcinogenesis, due to the strong inflammatory response that is generated upon exposure to such cells.

The aim of this thesis was to investigate the roles of folate and polymorphisms in folate metabolising genes in the aetiology of colorectal cancer.  The objectives were to: (1) conduct systematic reviews of (a) folate and colorectal neoplasia and (b) polymorphic genes in the folate pathway and colorectal neoplasia; (2) undertake a case-control study of folate, polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene and colorectal cancer in the north-east of Scotland; and (2) re-analyse the study data as if it were from a case-only study, comparing the results with those of the case-control analysis. The first systematic review concluded that there was considerable evidence that folate status modulates the risk of developing colon cancer, adenomatous polyps and, possibly, rectal cancer.  The risk reduction in the highest compared to the lowest intake group, for colon cancer and adenomas, was in the region of 30-40%. The second systematic review considered polymorphisms in MTHFR, methionine synthase (MTR), methionine synthase reductase (MTRR), cystathionine beta-synthase (CBS) and thymidylate synthase (TS).  Homozygosity for the MTHFR 677TT and 1298CC variants was associated with moderately reduced colorectal cancer risk in the majority of studies.  There was evidence of gene-environment interaction; in four of five studies, the lowest cancer risk was in 677TT subjects who had higher folate levels (or a “high methyl diet”) while in three studies 677TT homozygotes with the highest alcohol intake had the highest cancer risk.  The available evidence on MTHFR C677T and adenomatous polyps was inconclusive. A population-based case-control study of colorectal cancer was undertaken in Grampian health board area.  Eligible cases were Grampian residents diagnosed with histologically confirmed primary colorectal cancer during September 1998-February 2000. The primary analysis focused on all colorectal cancer.  Disease risk followed an inverted “U” pattern with increasing (total and dietary) folate intake.  There was little evidence of relations between disease and intakes of total or dietary vitamin B₁₂, vitamin B₆ or riboflavin or of interactions between these factors and folate.  There was a suggestion that protein intake was inversely related to colorectal cancer, which also drove the observation of a modestly increased risk with low, as compared to high, methyl intake (a combination of folate, protein and alcohol intake).  A modest, non-significant, reduction in risk was found in those with the 677 TT, compared to the CC, genotype.  For A1298C, a slight, non-significant, reduction in risk for homozygotes for the variant allele was found.  Significant interactions between the two polymorphisms and total folate intake were observed, although the patterns of interaction were different for each variant and not entirely consistent with published studies.

The aim of this thesis was to investigate the involvement of the insulin-like growth factor- and the one-carbon metabolism pathways in prostate cancer aetiology, studying both circulating biomarkers and genetic variation. Papers included in the thesis were conducted within the case-control study CAncer Prostate in Sweden (CAPS), and the two prospective studies European Prospective Investigation into nutrition and Cancer (EPIC), and Northern Sweden Health and Disease Cohort (NSHDC). In paper I, we investigated the relation between genetic variants of the IGF1 gene and prostate cancer risk within the CAPS study. We found that a common haplotype within the 3’ region of the IGF1 gene is associated with increased prostate cancer risk. In paper II, we investigated if the variants of the IGF1 gene that were associated with prostate cancer risk in paper I, are also associated with circulating levels of IGF1. Circulating levels of IGF1 were analysed in controls from the CAPS study and three haplotype tagging SNPs (htSNPs) were genotyped in subjects from the NSHDC study in which circulating IGF1 had previously been analysed. The genetic variants previously associated with increased prostate cancer risk were now also found to be associated with elevated levels of circulating IGF1. We concluded that variation in the 3’ region of the IGF1 gene affects prostate cancer risk by influencing circulating levels of IGF1. In paper III, we investigated if variants of the IGFBP1, IGFBP3 and IGFALS genes are associated with i) prostate cancer risk, ii) circulating concentrations of total and intact IGFBP3, and iii) prostate cancer-specific survival probability. In addition, we investigated if circulating concentrations of total and intact IGFBP3 are associated with prostate cancer-specific survival probability. No association between genetic variation and overall prostate cancer risk or survival was observed, but we found a strong association between elevated levels of intact IGFBP3 and increased risk of prostate cancer-specific death. We could, however, not exclude that this association was confounded by treatment or by the tumour. In paper IV, we investigated if circulating levels of folate and vitamin B12 are associated with prostate cancer risk within the EPIC study. We observed no associations between levels of folate, vitamin B12 and overall prostate cancer risk, but elevated levels of vitamin B12 were associated with increased risk of advanced stage disease. In paper V, we investigated if circulating levels of ten B-vitamins and related metabolites within the one-carbon metabolism pathway are associated with prostate cancer risk within the NSHDC study. Overall positive associations with prostate cancer risk were observed for levels of choline, vitamin B2 and vitamin B12, and inverse associations were observed for levels of homocysteine and MMA. We also observed a biologically plausible risk modification by smoking status on the association between vitamin B12 and risk; in non-smokers vitamin B12 was positively associated with risk, whereas the association between vitamin B12 and risk was inverse or null in ever/current-smokers. In summary, our results suggest that genetic variation of the IGF1 gene affects prostate cancer risk by affecting circulating levels of IGF1. The association between circulating concentrations of intact IGFBP3 and prostate cancer-specific survival is intriguing, but further studies are needed to conclude if this association is caused by confounding. We also observed associations between several factors of one-carbon metabolism and risk, but these associations were statistically week and require confirmation in other prospective studies.

The aims of this thesis were to describe the genesis, mediators and clinical sequelae of systemic inflammation in patients with gastro-oesophageal cancer. A consecutive series of 220 patients with gastric or oesophageal cancer were studied. Systemic inflammation (CRP>10 mg/l) was present in 43% of patients with gastro-oesophageal cancer. Serum acute phase protein concentrations (especially CRP), but not serum cytokine concentrations, were robust measures of systemic inflammatory activity. However, concentrations of pro-inflammatory cytokines within tumour tissue were significantly elevated and were linked with markers of systemic inflammation. IL-1β in particular was over-expressed in tumour tissue and may be a key determinant of systemic inflammation in patients with gastro-oesophageal malignancy. A chronic inflammatory cell infiltrate into the tumour tissue was present in 75% of tumours and was also linked with markers of systemic inflammation. Tumour cells or host immune cells or a combination of the two may be the main source of these mediators. The presence of systemic inflammation was also influenced by host cytokine genotype. Other potential tumour-derived mediators, such as PIF and PTHrP, may also play a (minor) role in the generation of systemic inflammation. CRP concentrations were identified as the best marker of prognosis and the magnitude of serum CRP concentrations were negatively liked with survival duration. 83% of patients had lost weight at the time of diagnosis and within 3 months this had increased to 92%. Increasing weight loss was positively associated with serum markers of systemic inflammation. Weight loss among patients with gastro-oesophageal cancer was not accounted for entirely by reduced food intake or mechanical obstruction secondary to the tumour. Alternatively, the presence of systemic inflammation contributed to nutritional decline (estimate of effect 34%). Weight loss was associated with adverse outcome and cachexia may be an aetiological factor involved in the link between systemic inflammation and adverse prognosis. Systemic inflammation, weight loss, performance status, and stage of disease were the main determinants of outcome in patients with gastro-oesophageal cancer. These factors were used to devise a novel model to improve prognostic accuracy. These studies identify systemic inflammation as both an important prognostic indicator and a potential therapeutic target.

Introduction: Little is known about the aetiology of cancer in teenagers and young adults (TYA) aged 15-24 years, although in England, cancer is the most common cause of disease-related mortality in this age group. The most common cancers at this age are lymphomas, central nervous system (CNS) tumours and germ cell tumours (GCT). The commonest carcinomas seen at older ages including lung, breast, large bowel and prostate account for only 3-4% of TYA cancers. In this thesis I describe the incidence patterns of selected cancers in TYA and the variation seen with geography, time and in population subgroups. The focus is on CNS tumours, GCT and bone tumours as they either peak in incidence in TYA and/or contribute disproportionately to cancer related mortality in TYA. This will allow formulation of hypotheses regarding aetiology of cancer in this age group which can then be tested by further research. Methods: For the majority of the analysis, anonymised national cancer registration data from England on individual patients of all ages with newly diagnosed cancer between 1979 and 2003 were used. To contrast the incidence patterns in England with that of India, data from five Indian urban population based cancer registries were used for part of the analysis. Age, sex, site and histology specific incidence rates were calculated and expressed per million person years. All rates, where appropriate, were adjusted to the world standard population using direct methods. To explore the link of growth with development of osteosarcoma and Ewing sarcoma, a random-effects meta-analysis was undertaken on studies which investigated an association of these tumours with height at diagnosis. Results: The incidence of cancer in TYA overall in England exceeded that of India. This was also true for most individual sites including epithelial cancers of lung, colon/rectum, breast, ovary and cervix, and non-epithelial cancers including melanoma, Hodgkin lymphoma and testicular cancer. Notable exceptions to this pattern were cancers of the mouth, gall bladder and stomach (females only) where incidence was higher in India. In England, CNS tumours in TYA were a composite of pilocytic astrocytomas and embryonal tumours (representing tail end of childhood CNS tumours), pituitary tumours, nerve sheath tumours, high grade astrocytomas and meningiomas (representing early-onset of CNS tumours that peak in incidence in the 6th and 7th decade of life), and of CNS GCTs, pleomorphic xanthoastrocytomas and neurocytomas which show a peak incidence in TYA. Irrespective of site or histology, GCT in England showed a peak in incidence between ages of 10 to 39 years which was more marked in males. This however varied by site and the peak incidence was seen at 10 to 14 years in the CNS, 15 to 19 years in ovary, 25 to 29 in mediastinum & thorax and abdomen & pelvis, and 30 to 34 years in testicular tumours. Osteosarcoma and Ewing sarcoma were the predominant bone tumours in TYA in England and showed a distinct peak of incidence at 10 to 14 years age in females and a larger peak at 15 to 19 years age in males. The peak incidence of osteosarcoma of long bones of the lower limb was six times more than that at any other site while the peak incidence of Ewing sarcomas located in the bones of the central axis exceeded those in long bones of the lower limb. The average height of patients with osteosarcoma at diagnosis was found to be significantly above the average height of the reference population, at the 95% level. The association of greater height at diagnosis with Ewing sarcoma was also significant at the 95% level but much weaker. Conclusion: In this thesis I have explored the epidemiology of cancer in TYA using some of the established methodologies which have previously been used in advancing our knowledge of childhood and older adult cancers. These studies provide some clues to aetiology. Variation in environmental exposures and lifestyle factors between England and India can explain the majority of the differences in incidence patterns observed. Genetic predisposition to cancer along with carcinogen exposure could lead to early onset of some cancers generally seen in older adults. Regardless of site, the similarity in age-incidence patterns of GCT, suggests a common initiation of these tumours in embryonic/foetal life with variable rates of tumour progression as a result of local factors or events during postnatal and pubertal period. The incidence patterns of osteosarcoma along with the strong and consistent association with a greater height at diagnosis indicate that bone growth is important in the development of this tumour while different biological pathways which may be unrelated to growth could also be relevant for Ewing sarcoma.

California sea lions (CSLs) have an unusually high occurrence of urogenital cancer (UGC), with studies revealing metastatic carcinoma in 26 % of CSLs admitted to a rehabilitation centre between 1998 and 2012. It is likely that the aetiology of this disease is multi-factorial as genetics, viral infection and exposure to contaminants have been associated with this cancer to date. The goal of this study was to investigate the association of a number of factors using a case-control study design on animals admitted to a rehabilitation centre. The study additionally concentrates on two main areas; (i) genetic factors and (ii) the presence of herpesvirus. Previous investigations identified cancer to be more likely in animals with specific microsatellite alleles. In the present study genotyping of CSLs at three microsatellite loci revealed that homozygosity at one marker (Pv11) was significantly associated with the presence of the disease. Pv11 was found to be located within a gene called heparanase 2 (HPSE2) and investigations into the expression of its protein revealed differences according to Pv11 genotype. The presence of herpesvirus was investigated by two PCR methods and identified the gammaherpesvirus OtHV-1. The results of the two methods were contradictory with one method identifying a highly significant relationship between the presence of OtHV-1 and UGC whereas the other did not. Complicating factors such as potential differences in sensitivity of the tests along with the possible presence of closely related viruses or variants of OtHV-1 may explain this. The availability of necropsy data for the CSLs in the study allowed the inclusion of body condition data in the statistical analysis to evaluate other potential risk factors. Final analysis revealed the presence of three risk factors; Pv11 genotype, OtHV-1 presence and thinner blubber. This study is the largest study undertaken so far in order to investigate the involvement of risk factors associated with UGC in the CSL and supports a multi-factorial aetiology of this disease.

The cancers of the skin, melanoma and the keratinocyte cancers, basal cell andsquamous cell carcinomas (BCC and SCC), are among the most common cancersin white populations. While ultraviolet radiation (UVR) is their principal cause,links with non-UVR-related factors have also been noted. Ultimately, theinteraction of these elements results in malignancy however, understanding oftheir specific contributions remains incomplete. This thesis reports findings fromsix studies aiming to investigate gaps in current knowledge of the role of UVR andnon-UVR-related risk factors on skin cancer. The papers are groupedaccording to the aspects of skin cancer epidemiology and aetiology they address. The first two papers address the descriptive epidemiology of melanoma inEngland, a country with low ambient solar UVR. They arise from ecologicalstudies using national melanoma registration data and document rising trends inmelanoma incidence by anatomic site (Paper 1), and by region of residence andsocio-economic deprivation (Paper 2). Their findings were consistent with thesuggestion that increases in recreational UVR exposure are driving rises inmelanoma rates. These results emphasise both the need to closely monitor UVRexposure and melanoma trends and the importance of public health campaigns. The second group of three papers considers the assessment of associations ofnutritional factors with keratinocyte cancer. Two studies use data from aprospective cohort to evaluate the relationship between dietary intake (Paper 3)and blood concentrations (Paper 4) of omega-3 and omega-6 polyunsaturatedfatty acids (PUFA) in relation to BCC and SCC risk. Associations with both PUFAtypes were observed. In addition, Paper 5, a three-way correlational assessment,demonstrated that questionnaire and blood circulating levels of omega-3 PUFAwere highly correlated with measures of skin bioavailability. Collectively, thesestudies give evidence for associations of these nutrients with skin cancer and forthe utility of both intake and biomarker measures for assessing the relationships. The final paper explores the relationship between a widely cited non-UVR riskfactor, namely scars and cancers of the skin. It reports a systematic review of allpublished observational studies quantifying this association. While innumerablecase reports were found, quantitative analyses were rare. The review identifieda major gap in the literature where knowledge of scar malignancies is notevidence-based, but rather founded mainly on cumulative anecdotal reporting. Taken together, this body of published work highlights the largely unrecognisedcomplexity of the aetiology of cancers of the skin. Future research must bebroad in scope in order to advance understanding of the interaction betweenUVR and other risk factors and to provide a base for health messages aimed atreducing the burden of these malignancies.

This thesis consists of three main parts. An introduction to diode-pumped solid-state lasers, thermal modelling of solid-state lasers and rate-equation modelling of solid-state lasers. The first part explains the basic components and operation principles of a typical diode-end-pumped solid-state laser. The stimulated emission process, solid-state laser gain media, various pump geometries and a basic end-pumped laser resonator configuration are among the topics that are explained. Since thermal effects are one of the main limiting factors in the power-scaling of diode-pumped solid-state lasers, the second part of this thesis describes numerical and analytical thermal models that determine the thermal lens and thermally induced stresses in a laser crystal. As a first step, a time-independent numerical thermal model which calculates the three-dimensional temperature distribution in the laser crystal is implemented. In order to calculate the time dependent thermally induced stresses in a laser crystal, a coupled thermal-stress finite element analysis model was implemented. Even though some steady-state analytical solutions for simple crystal geometries do exist, the finite element analysis approach was taken so that the time dependent thermally induced stresses could be calculated for birefringent crystals of various geometries. In order to validate the numerical results, they are compared to experimental data and analytical solutions where possible. In the last part, the population dynamics inside the laser gain medium are described and modelled with a quasi-three-level rate-equation model. A comprehensive spatially resolved rate-equation model is developed and discussed. In order to simplify the implementation of the rate-equation model as a computer simulation, the spatial dependence of the laser parameters is ignored so that the model reduces to a singleelement plane-wave model. The simplified rate-equation model is implemented and solved numerically. The model is applied to a four-level CW and Q-switched Nd:YLF laser as well as a quasi-three-level QCW Tm:GdV04 laser. The models' predictions are thoroughly verified with experimental results and also with analytical solutions where possible.
Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Durban, 2007.

The central nervous system is a potential site of action for the Fusarium mycotoxin Fumonisin B1 (FB1), and is exemplified in horses by the disease equine leukoencephalomalacia. Structurally resembling sphingoid bases, FB1 inhibits ceramide synthase, an enzyme involved in sphingolipid metabolism, leading to accumulation of free sphinganine (Sa) and sphingosine (So). This investigation focused on FB1, Sa, So and the Fusarium mycotoxins fusaric acid (FA), moniliformin (MaN), zearalenone (ZEA), deoxynivalenol (DON), and T-2 toxin (T2). Effects of the Fusarium mycotoxins and sphingoid bases on the N2a neuroblastoma cell line were assessed using the methylthiazol tetrazolium (MIT) and ApoGlow™ assays. The MIT assay revealed significant differences between the viability of N28 control cells and the cytotoxic effects of FB1 (p=0.001), So (p=1.1 x10-6 ), Sa (p=1.9x10-6 ), MON (p=0.002), DON (p=0.04) and ZEA (p=0.003) on N28 cells between 5-250µM. The cytotoxic effects of FA did not differ significantly from controls (p=0.1). The ApoGlow™ assay revealed that in N28 cells, FB1 at 8µg.ml-1, FA at 128µg.ml-1, and (FBI+FA) combined induced growth arrest at 2 and 4µg·ml-1. Assessment of the effects of FBI and FA on the Jurkat leukaemic suspension cell line revealed that FB1 induced apoptosis at 1.56,12.5 and 50µ.ml-1, growth arrest at 100, 200 and 800µg.ml-1 and proliferation at 400µg.mg-1. Fusaric acid induced proliferation at 1. 56µg.ml-1, apoptosis at 3.15µg.mrl, growth arrest at 100 and 200µg.mrl, and necrosis at 800µg.ml-1. Combined, (FB1+FA) induced apoptosis at 1.56, 3.15,12.5 and 800µg.ml-1. Flow cytometry and fluorescence microscopy revealed that mycotoxins, Sa and So induced varying levels of apoptosis and necrosis in N28 cells. Acridine orange and ethidium bromide staining facilitated discrimination between viable, apoptotic and necrotic cells. Transition of the mitochondrial transmembrane potential was measured using Rhodamine 123 with propidium iodide, and the dual emission potential sensitive stain JC-1. Changes in mitochondrial membrane potential and plasma membrane integrity were expressed as increases or decreases in fluorescence intensity. An increase in mycotoxin concentration from 50 to 200µM was usually paralleled by a decrease in J-aggregate formation, suggesting a decrease in the ?¦¥m. Staining with Rh 123/PI indicated at specific concentrations whether N28 cells were either late apoptotic or necrotic reflected by the levels of PI uptake. No dose dependant mechanism of cell death was established using either method, as fluctuations were evident. Immunolocalisation of T2, ZEA and FB1 within cellular organelles that exhibited ultrastructural pathology provided correlation between mycotoxin exposure and effects. Multinucleate giant cells and retraction of cellular processes were observed. At the electron microscope (EM) level, FB1 was immunolocalised within microsegregated and peripherally condensed nucleoli, the nucleoplasm, distorted mitochondria and dilated endoplasmic reticulum (ER). The capacity of cells to incorporate mycotoxins and effect cytological changes represents a major factor in the potential for initiation of malignant transformation. Exposure of N2a cells to FB1 for 72 hours increased intracellular free Sa and depleted complex sphingolipids. Using High Performance Liquid chromatography (HPLC), acid hydrolysis revealed reduction in Sa from a level of O.6±0.12µM in control cells, to 02±0.lµM in cells exposed to 50µM and lOOµM FB1. Base hydrolyses revealed increase in free Sa: So ratios from 0.52±0.2 in control cells, to 1.14±0.2 and 1.4±0.3 in cells exposed to 50 and l00µM FB1 respectively. The Sa: So ratio in the complete culture media (CCM) increased from 1. 7±0. 3 for control cells to 2.0±0.2 and 2.50±0.4 for cells exposed to 50 and lOOµM FB1 respectively. Correlation coefficients between Sa: So ratios to FB1 exposure in CCM (R=0.75) and within cells (R=0.85), imply that the free Sa: So ratio within cells appears to be a better biomarker for FB1-induced disruption of sphingolipid metabolism in vitro, than the Sa: So ratio in CCM. Optimisation of HPLC analytical procedures improved recovery of FB I from spiked human sera to 95.8% (n=15) and detection limits to -5ng.ml-1 at a signal to noise ratio of 5:1. Optimisation of methods for recovery of Sa and So from spiked sera, led to recoveries of 77.9% and 85.0%, for So and Sa respectively at levels of spiking with lOng per 500µl of serum. Matched sera Sa:So ratios and FB1 levels in brain cancer and non-cancer subjects in KwaZulu-Natal were determined using these optimised methods. Fumonisin B1 was detected in sera of non-cancer (76.7±62.2nM) and brain cancer subjects (l07.38±116nM). Mean serum Sa:So ratios of 21 non-cancer subjects was 1.7±0.7. There was no correlation (R=0.26) between these variables in non-cancer subjects. The mean serum FB1 level in brain cancer subjects was 107.4±116nM (range 10.5-298nM) (n=50) and the mean Sa:So ratio (n=50) was 1.9±1.7 (range 0.40-8.16). No correlation was found between these variables in the brain cancer subjects either (R = -0.23). Fumonisin B1 was irnmunolocalised in 49 of 76 brain tumour tissue samples analysed using immunohistochemistry (IHC). Thirty-eight of the 76 specimens had matched serum FBI levels and Sa: So ratios, and 23 of these were positive for FB1 presence. Although not significantly different (p=0.ll), the FBI sera levels in the cancer group with FBI within the tumour tissue had higher levels of FB1 in sera than the IHC FB1 negative group. Fumonisin B1 was localised within irregular profiles of nuclei, elongated and swollen mitochondria and ER. Immunolocalisation of FB1 within organelles in the brain showing ultrastructural cellular pathology suggests FBI may be implicated in the aetiology of human brain carcinogenesis.
Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2004.

2015 Dissertation submitted to the Faculty of Health Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Medicine.
Hereditary breast cancer (HBC), caused by mutations in tumour suppressor genes, has been well studied in Caucasian and Ashkenazi Jewish populations. Little is known about the genetic aetiology or the clinical epidemiology of HBC in African and South African black populations. Founder mutations within specific genes have been described for numerous populations worldwide. In South African black women, breast cancer often presents with early age of onset, rapid progression of disease and adverse histological phenotypes. It is possible that mutations within already described HBC-associated genes account for this phenotype in the South African black population. Genetic mutations within the BRCA1 and BRCA2 genes contribute to the development of breast cancer in high-risk cancer patients internationally. The proportion of breast cancers caused by mutations in the BRCA1 and BRCA2 genes in the local black population is currently not well understood. This study screened 33 South African black women presenting with early onset, high-risk breast cancer, for genetic mutations in the BRCA1 and BRCA2 genes. These individuals were selected on predefined high-risk criteria, including early age of disease onset, family history and cancer histology. Mutation screening was done using bi-directional Sanger sequencing of the exons of both genes, and MLPA analysis. A total of 59 distinct single nucleotide variants were found in the BRCA1 and BRCA2 genes. Three of these variants are pathogenic or likely pathogenic (BRCA1: c.431dupA; BRCA2: c.582G>A & c.7712A>G). Five novel variants with unknown clinical significance were also found (BRCA1: c.3751T>G, c.306A>C, c.5332+78C>T, c.212+66A>G; BRCA2: c.681+10T>G). There is little evidence to suggest that these novel variants are likely to have a functional impact and to be pathogenic. The remaining 51 variants were previously reported. No large gene/exon deletions or duplication mutations were found on MLPA analysis. The allele frequency data of the 51 previously reported variants were compared to the allele frequencies of two separate control groups: an ethnically matched control group (established and investigated in-house by a previous Masters student in the Division) and the 1000 genomes project data. This comparison was done to screen for tag SNPs for future genetic association studies in black South Africans and to evaluate potential background genetic differences within the BRCA genes of different African populations. One allele within the BRCA1 gene occurred at a frequency which was statistically significant as compared to the normal South African black population and one allele within the BRCA2 gene was statistically significant. The two control groups were also compared against each other. The allele frequencies were significantly different between the two control groups, suggesting that other African population groups (1000 genomes project data) do not serve well as control groups for sub-Saharan African populations. Genetic mutations within the BRCA1 and BRCA2 genes account for approximately 10% (3/33) of the breast cancer cases within this high-risk cohort. Thus, the proportion of BRCA mutations contributing to the development of inherited breast cancer in sub-Saharan blacks appears to be in keeping with data reported for other ethnic groups. No evidence of any founder mutation/s was evident, although the sample size tested here was too small to exclude their existence.

The purpose of the study has been primarily to draw a profile of malignant melanoma in the different population groups inhabiting the Natal Province and Kwa-Zulu, to compare the presentation and incidence of the disease between these groups as well as with similar racial groups in different countries. The data collected then permitted to estimate which parameters were relevant in predicting the course of the disease, as well as the results of surgical and adjuvant therapy, and was utilized in a search for the aetiology of the tumour.
Thesis (M.D.)-University of Natal, Durban, 1985.

Thyroid cancer is the most common malignancy of the endocrine system. The majority of thyroid cancers derive from the follicular cells, being designated as non-medullary thyroid carcinomas (NMTC). NMTC also occurs in a familial form, entitled familial non-medullary thyroid carcinoma (FNMTC), representing 3-9% of all thyroid cancers. FNMTC is currently defined by the diagnosis of two or more first degree relatives with differentiated thyroid cancer of follicular cell origin. The family members frequently present benign lesions of the thyroid, such as multinodular goiter (MNG). Several FNMTC susceptibility genes have been reported, such as NKX2.2, FOXE1 and DICER1, but these are mutated only in a small fraction of families. Thus, the molecular basis of FNMTC is still mostly unknown, being regarded as a genetically heterogeneous disease. Recently, germline truncating mutations in DNA repair-related genes have been described in cases of thyroid cancer. In addition, activating mutations in BRAF and RAS oncogenes have been reported to be involved in familial thyroid tumour progression. In order to further clarify the molecular basis of FNMTC, the main goal of this project was to identify novel susceptibility gene(s) for this disease. To achieve this aim, three different approaches were used: the study of a very representative family of our cohort (six affected members with NMTC) through wholeexome sequencing (WES); the analysis of 94 genes associated with hereditary cancer predisposition in 48 probands from FNMTC families, through next-generation sequencing (NGS), using a commercial panel (Trusight Cancer Kit); and the analysis of the candidate genes telomerase reverse transcriptase (TERT) and eukaryotic translation initiation factor 1A X-linked (EIF1AX), selected based on previous evidence for their involvement in familial and/or sporadic thyroid cancer. The analysis of the FNMTC family with six-affected members through WES generated above 300,000 variants for each sample. Significant variants were selected through bioinformatics analysis, sets of filters, and validated using Sanger sequencing. In silico prediction, literature and database search of gene function and expression, were used to select potentially pathogenic variants, which was followed by analysis of their segregation with the disease in the family. The variant (c.701C>T, p.Thr234Met) in SPRY4 gene was prioritised for functional studies. To disclose the contribution of this variant to thyroid tumourigenesis, functional studies were performed using three cell models (NIH/3T3, PCCL3 and TPC-1). Overall, mutant SPRY4, compared to the wild-type, induced an increase in cell proliferation/viability, colony formation and in phosphorylation levels of proteins involved in MAPK/ERK and PI3K/AKT pathways. These results are in accordance with the well-established role of these signalling mechanisms in thyroid tumour development. Overall, these data suggested, for the first time, a role for SPRY4 in familial thyroid cancer initiation. In the NGS analysis of 94 genes in the 48 probands from FNMTC families, a total of 20,160 variants were identified. In silico analysis of NGS data unveiled 47 likely pathogenic germline variants in genes involved in DNA repair (33 variants) and in other hereditary cancer predisposing genes (14 variants). From these variants, only 18 segregated with FNMTC in 13 families, of which 15 variants were in DNA repair genes (APC, ATM, CHEK2, ERCC2, BRCA2, ERCC4, FANCA, FANCD2, FANCF, BRIP1 and PALB2), two in DICER1, and one in RHBDF2. These results reinforced the relevance of DNA repair genes and DICER1 in FNMTC aetiology and extended the present knowledge, by suggesting CHEK2, ERCC4, FANCA, FANCD2, FANCF, PALB2, BRIP1 and RHBDF2 as susceptibility genes for this disease. The main mechanisms involved in DNA repair, which may be altered according to this study, include the repair of double-strand breaks by homologous recombination (CHEK2, ATM, BRIP1, BRCA2, FANCD2 and PALB2 genes) and by DNA interstrand crosslink repair (FANCA and FANCF genes); the other mechanisms include repair of single-strand breaks by nucleotide excision repair (ERCC4 and ERCC2 genes) and by base excision repair (APC gene). In the approach that involved the direct study of candidate genes in FNMTC, using Sanger sequencing, no potentially pathogenic germline variants were identified in the TERT promoter in the 75 FNMTC families’ probands. However, in 54 familial thyroid tumours studied, we identified mutations in TERT promoter (9%), BRAF (41%), and RAS (7%), but no mutations were identified in EIF1AX. TERT-positive samples were also positive for BRAF, and this co-occurrence was statistically significant (p=0.008). In addition, TERT mutations in concomitance with BRAF mutations, had a significant correlation with more advanced tumour stages (T4) (p=0.020). This study showed that TERT promoter mutations are not frequently involved in FNMTC aetiology, but rather implicated in tumour progression and aggressiveness, when coexisting with BRAF mutations. Overall, we have identified novel susceptibility genes that are likely to participate in FNMTC tumourigenesis: SPRY4 seems to explain thyroid cancer aetiology in the FNMTC family studied and DNA repair genes may also be involved in FNMTC initiation. The oncogenic role of RAS and BRAF mutations in familial thyroid tumour progression was confirmed, and coexistent mutations in TERT promoter and BRAF were, for the first time, implicated in the progression and aggressiveness of FNMTC. This study improved the present knowledge of the genetic basis of FNMTC and further supported that this is a genetically heterogeneous disease. The identification of these genes involved in the initiation and progression of FNMTC, if supported by future studies in other cohorts, may allow families with this disease to undergo early diagnosis, and improve the clinical management of these patients.
O carcinoma da tiróide é a neoplasia mais comum do sistema endócrino. A maioria dos carcinomas da tiróide deriva das células foliculares, sendo designados carcinomas nãomedulares da tiróide (NMTC). Os NMTC podem apresentar-se como forma familiar, que é denominada FNMTC (carcinoma não-medular da tiróide familiar), representando 3 a 9% de todos os carcinomas da tiróide. O FNMTC é definido pelo diagnóstico de dois ou mais familiares em primeiro grau com carcinoma da tiróide de origem folicular. Frequentemente os familiares apresentam lesões benignas da tiróide, como o bócio multinodular (MNG). Embora tenham sido mapeados e identificados alguns genes de susceptibilidade para o FNMTC (e.g. NKX2.2, FOXE1 e DICER1), estes encontram-se alterados apenas numa reduzida fracção das famílias. Desta forma, a base molecular do FNMTC permanece essencialmente desconhecida, sendo considerada uma doença geneticamente heterogénea. Recentemente, foram descritas mutações germinais truncantes em genes de reparação do DNA em casos com cancro da tiróide. A progressão dos tumores da tiróide de origem familiar envolve a ocorrência de mutações somáticas activadoras nos genes BRAF e RAS. De modo a clarificar a base molecular do FNMTC, o objectivo principal deste projecto foi identificar novo(s) gene(s) de susceptibilidade para esta doença. De modo a alcançar este objectivo foram utilizadas três abordagens diferentes: a análise por sequenciação global do exoma (WES) de uma das famílias mais representativas da série em estudo (seis membros afectados com NMTC); a análise de 94 genes que predispõem para cancro hereditário, em 48 probandos de famílias com FNMTC, através de sequenciação de nova geração (NGS), utilizando um painel comercial (Trusight Cancer Kit); por último, foram analisados dois genes candidatos, TERT e EIF1AX, seleccionados com base em evidências prévias do seu envolvimento no cancro familiar e/ou esporádico da tiróide. A análise através de WES de seis membros afectados da família com FNMTC, gerou mais de 300.000 variantes por cada amostra. As variantes mais relevantes foram seleccionadas através de análise bioinformática, uso de filtros específicos e validadas através da sequenciação de Sanger. Recorreu-se à predição in silico, pesquisa na literatura e em bases de dados sobre a função e expressão génica para seleccionar as variantes potencialmente patogénicas, e em seguida realizaram-se estudos da segregação das variantes com a doença na família. A variante (c.701C>T, p.Thr234Met) no gene SPRY4 foi priorizada para estudos funcionais. Efectuaram-se estudos funcionais em três modelos celulares (NIH/3T3, PCCL3 e TPC-1) para avaliar a possível contribuição desta variante para a tumorigénese na tiróide. Observou-se que a variante induzia um aumento na proliferação/viabilidade celular, na formação de colónias e nos níveis de fosforilação de proteínas envolvidas nas vias MAPK/ERK e PI3K/AKT. Estes dados estão de acordo com o papel bem estabelecido para estes mecanismos de sinalização no desenvolvimento dos tumores da tiróide. Concluindo, estes resultados sugeriram, pela primeira vez, um papel para o gene SPRY4 na iniciação tumoral do cancro da tiróide familiar. Na análise dos 94 genes através de NGS nos 48 probandos das famílias com FNMTC, identificou-se um total de 20.160 variantes. Os dados da análise in silico do NGS revelaram 47 variantes germinais potencialmente patogénicas, em genes envolvidos na reparação do DNA (33 variantes) e noutros genes relacionados com a predisposição para o cancro hereditário (14 variantes). Destas variantes apenas 18 segregaram com a doença em 13 famílias, das quais 15 variantes ocorriam em genes de reparação do DNA (APC, ATM, CHEK2, ERCC2, BRCA2, ERCC4, FANCA, FANCD2, FANCF, BRIP1 and PALB2), duas no gene DICER1 e uma no gene RHBDF2. Estes resultados reforçaram a relevância dos genes de reparação do DNA e do gene DICER1 na etiologia do FNMTC, contribuindo para o conhecimento actual através da identificação de genes, tais como o CHEK2, ERCC4, FANCA, FANCD2, FANCF, PALB2, BRIP1 e RHBDF2, como estando possivelmente envolvidos na susceptibilidade para esta doença. Os principais mecanismos envolvidos na reparação do DNA, que foram identificados como estando alterados neste estudo, incluem a reparação da quebra da dupla cadeia de DNA através de recombinação homóloga (genes CHEK2, ATM, BRIP1, BRCA2, FANCD2 e PALB2) e a reparação do tipo “interstrand crosslink” do DNA (genes FANCA e FANCF); os outros mecanismos incluem a reparação da quebra da cadeia simples de DNA por excisão de nucleótido (genes ERCC4 e ERCC2) e por excisão de base (gene APC). Na abordagem que envolveu o estudo directo de genes candidatos para FNMTC, utilizouse a sequenciação de Sanger, não tendo sido identificadas variantes potencialmente patogénicas a nível germinal no promotor do TERT, nos 75 probandos das famílias estudadas. Contudo, nos 54 tumores da tiróide dos familiares estudados identificaram-se mutações no promotor do TERT (9%), BRAF (41%) e RAS (7%), não tendo sido identificadas mutações no gene EIF1AX. As amostras positivas para o TERT também eram positivas para o BRAF, sendo esta co-ocorrência estatisticamente significativa (p=0.008). Além disso, as mutações no gene TERT em concomitância com mutações no gene BRAF revelaram uma correlação significativa em estádios mais avançados do tumor (T4) (p=0.020). Este estudo demonstrou que as mutações no promotor do TERT não estão envolvidas na etiologia do FNMTC, mas sim implicadas na progressão e agressividade tumoral, quando coexistem com mutações no BRAF. Concluindo, identificaram-se genes que poderão estar envolvidos na tumorigénese do FNMTC. O gene SPRY4 poderá explicar a etiologia dos tumores da tiróide na família com FNMTC estudada e os genes de reparação do DNA parecem estar implicados na iniciação do FNMTC em diferentes famílias. Confirmou-se o papel oncogénico dos genes RAS e BRAF na progressão dos tumores da tiróide de origem familiar e, pela primeira vez, demonstrou-se que a coexistência de mutações no promotor do TERT e no BRAF está relacionada com a progressão e agressividade em FNMTC. O presente estudo incrementou o conhecimento actual sobre a base genética do FNMTC e corroborou que se trata de uma doença geneticamente heterogénea. A identificação destes genes envolvidos na iniciação e progressão do FNMTC, se suportado por estudos noutras séries, poderá permitir que famílias com esta doença tenham acesso a um diagnóstico precoce, facilitando o manejo clínico dos doentes.