High mobility group nucleosome binding (HMGN) proteins belong to the superfamily of high mobility group (HMG) proteins. HMGN1 and HMGN2 are ubiquitously expressed in all vertebrates, and are most highly expressed in embryonic tissue. Moreover, HMGN1 and HMGN2 were found to be highly expressed in neural stem/progenitor cells in the mouse brain. Here, mouse embryonal carcinoma cells (P19 EC) were used as a model system to study the role of HMGN proteins in pluripotent stem cells. Previously, experiments using short interfering RNA (siRNA) technology to knockdown HMGN1 and HMGN2 have suggested that HMGN proteins are important for the expression of key pluripotent genes, Oct4, Sox2 and Nanog, in P19 EC cells (Mohan, 2012). The aim of this thesis was to develop a lentiviral system for the long term knockdown of Hmgn2, in order to investigate more fully the role of this protein in stem cell pluripotency and differentiation. Constitutive and inducible lentiviral shRNAmir systems were tested and optimized, and a constitutive system was chosen for further work. HMGN2 knockdown in undifferentiated P19 EC cells resulted in the down-regulation of Oct4 protein levels. ChIP assays showed that HMGN2 binding over the Oct4 gene was absent in HMGN2 knockdown cells. Furthermore, binding of HMGN1 at this locus was increased in the absence of HMGN2. Consistent with the reduction in Oct4 expression, levels of the active histone modification, H3K4me3, were also decreased at the Oct4 gene. These results support a role for HMGN2 in the regulation of Oct4 expression in P19 cells, and imply that HMGN2 may be important for maintaining stem cell pluripotency.

Canonical WNT signalling plays a critical role in the regulation of ovarian development during embryogenesis; dysregulation of this pathway in adult ovary is associated with subfertility and tumourigenesis. The aim of the current study was to elucidate the previously unexplored roles of Adenomatous polyposis coli 2 (APC2), a WNT signalling pathway regulator, in the ovary using an Apc2 constitutive knockout mouse. For the first time, the current work demonstrated essential roles of APC2 in regulating ovarian WNT signalling and ovarian homeostasis. In early adulthood, APC2-deficiency resulted in WNT signalling activation and sub-fertility driven by intra-ovarian defects. Follicular growth was perturbed, resulting in a reduced rate of ovulation and corpora lutea formation, which was not rescued by administration of gonadotrophins. The current study provides fundamental new knowledge on the role of APC2 in ovarian tumourigenesis. APC2-deficiency (on the background of a hypomorph Apc- allele) resulted in a predisposition to granulosa cell tumour (GCT) formation, accompanied by acute tumour-associated WNT-signalling activation and expression of a histologic pattern and molecular signature seen in human adult GCTs. Hence, APC2 has an important tumour-suppressor activity within ovarian granulosa cells. However, APC2 is dispensable for ovarian surface epithelium (OSE) homeostasis. APC2 loss on its own, or combined with PTEN or APC loss in the OSE, failed to cause tumour development. Introducing APC2-deficiency to an ovarian endometrioid adenocarcinoma (OEA) mouse model, driven by loss of PTEN and APC in the OSE, resulted in early initiation of tumourigenesis, but attenuated tumour growth. This attenuation was accompanied by squamous metaplasia, decreased mitosis, decreased p-ERK1/2 expression and disrupted immune/inflammatory signalling. Thus, for the first time, an APC2 functional dualism in initiation and progression of WNT-driven OEA in mice is reported. RNA sequence analysis unraveled 2 transcripts (HAL and HUNK) associated with OEA progression and should be considered for future research.

When digital imaging and image processing methods are applied to clinical diagnostic and prognostic needs, the methods can be seen to increase human understanding and provide objective measurements. Most current clinical applications are limited to providing subjective information to healthcare professionals rather than providing objective measures. This Thesis provides detail of methods and systems that have been developed both for objective and subjective microscopy applications. A system framework is presented that provides a base for the development of microscopy imaging systems. This practical framework is based on currently available hardware and developed with standard software development tools. Image processing methods are applied to counter optical limitations of the bright field microscope, automating the system and allowing for unsupervised image capture and analysis. Current literature provides evidence that 3D visualisation has provided increased insight and application in many clinical areas. There have been recent advancements in the use of 3D visualisation for the study of soft tissue structures, but its clinical application within histology remains limited. Methods and applications have been researched and further developed which allow for the 3D reconstruction and visualisation of soft tissue structures using microtomed serial histological sections specimens. A system has been developed suitable for this need is presented giving considerations to image capture, data registration and 3D visualisation, requirements. The developed system has been used to explore and increase 3D insight on clinical samples. The area of automated objective image quantification of microscope slides presents the allure of providing objective methods replacing existing objective and subjective methods, increasing accuracy and rsducinq manual burden. One such existing objective test is DNA Image Ploidy which seeks to characterise cancer by the measurement of DNA content within individual cell nuclei, an accepted but manually burdensome method. The main novelty of the work completed lies in the development of an automated system for DNA Image Ploidy measurement, combining methods for automatic specimen focus, segmentation, parametric extraction and the implementation of an automated cell type classification system. A consideration for any clinical image processing system is the correct sampling of the tissue under study. VVhile the image capture requirements for both objective systems and subjective systems are similar there is also an important link between the 3D structures of the tissue. 3D understanding can aid in decisions regarding the sampling criteria of objective tests for as although many tests are completed in the 2D realm the clinical samples are 3D objects. Cancers such as Prostate and Breast cancer are known to be multi-focal, with areas of seeming physically, independent areas of disease within a single site. It is not possible to understand the true 3D nature of the samples using 2D micro-tomed sections in isolation from each other. The 3D systems described in this report provide a platform of the exploration of the true multi focal nature of disease soft tissue structures allowing for the sampling criteria of objective tests such as DNA Image Ploidy to be correctly set. For the Automated DNA Image Ploidy and the 3D reconstruction and visualisation systems, clinical review has been completed to test the increased insights provided. Datasets which have been reconstructed from microtomed serial sections and visualised with the developed 3D system area presented. For the automated DNA Image Ploidy system, the developed system is compared with the existing manual method to qualify the quality of data capture, operational speed and correctness of nuclei classification. Conclusions are presented for the work that has been completed and discussion given as to future areas of research that could be undertaken, extending the areas of study, increasing both clinical insight and practical application.

RNA Polymerase III (Poll III) contributes to about 10% of nuclear transcription and is essential for the synthesis of short untranslated transcripts, including tRNA and 5S rRNA. Pol III deregulation has been implicated in driving cellular proliferation and transformation, along with increased expression of a number of Pol III specific transcription factors and transcripts. The significance of Pol III in clinical pathology, including that of human malignancies, remains to be formally tested. Using prostate cancer as a model, two key components of the Pol III complex, namely Brf1 and tRNAiMet, were investigated. The expression patterns of Brf1 and tRNAiMet were studied in this thesis using immunohistochemistry (IHC) and in situ hybridisation (ISH) respectively. Brf1, a subunit of transcription factor IIIB (TFIIIB), was detected predominantly in the nucleus with heterogenous staining intensity, its presence ranging from weak to strong. Examination across a wide range of tissue types and organs, both normal and tumour tissues revealed high levels of Brf1 expression in the epithelium. In addition, Brf1 expression could also be detected in connective tissues and, to a lesser extent, in muscular and nervous tissues. A number of tumour types exhibited elevated expression of Brf1 protein relative to their normal control tissues. These included prostate adenocarcinoma, B-cell lymphoma and, interestingly, tumours arising from connective tissues (sarcoma, fibrosarcoma and chondrosarcoma). As expected, tRNAiMet expression, as revealed by ISH analysis, was mostly observed in the cytoplasm, although some nuclear staining was also present. Similar to Brf1, tRNAiMet expression was detected predominantly in epithelial tissues such as the skin epidermis, prostate gland and epithelial lining of the cervix. A number of tumours were found to overexpress tRNAiMet. These included breast ductal carcinoma, oesophageal carcinoma and melanoma. The clinical impact of Brf1 and tRNAiMet overexpression was examined using tissue microarrays (TMA) containing tissue samples obtained from patients with prostate cancer (PCa) and benign prostate hyperplasia (BPH). Collectively, data from two independent patient cohorts, Glasgow TMA: BPH (n=21), PCa (n=151) and Newcastle TMA: BPH (n=113), PCa (n=365), showed that Brf1 expression was upregulated in prostate cancer relative to BPH (p=0.0034). Brf1 expression was not found to be associated with the following clinical and biologic parameters: Gleason sum score (indicative of tumour differentiation and morphology, p=0.653); prostate specific antigen (PSA level, indicative of tumour bulk or volume, p=0.381) and Ki-67 expression (signifying cellular proliferation, p=0.034). However, and importantly, within the prostate cancer patient cohorts studied, high Brf1 expression was associated with a significantly less favourable survival outcome (Kaplan Meier analysis, p<0.001). Together, the data presented in this study support the relevance of Brf1 and tRNAiMet overexpression as part of Pol III deregulation in tumours, especially of epithelial origin. This study also suggests the potential application of Brf1 as a prognostic marker in cancer, however, this warrants a further study.

Recent evidence suggests that stem cells are important for cancer metastasis and that the epithelial-to-mesenchymal transition also involves a transition toward stemness. Current thinking suggests that lgr5, a 7-transmembrane spanning G-protein, also marks a certain population of stem cells capable of regenerating an intestinal crypt and that the specialised immune secretory paneth cell, is important for maintenance of the stem cell niche. We implicate fascin in regulating the balance of lgr5 stem cells during acute intestinal inflammation and in regenerating intestinal tissue. Fascin is an actin bundling protein that drives the assembly of filopodia through the cross-linking of actin filaments into straight bundles. Conserved from amoebas to man, fascin was originally purified from extracts of sea urchin oocytes and coelomocytes and later found in Drosophila as the singed gene product. It is involved in the invasion and metastasis of multiple epithelial cancer types through stabilisation of actin in invadopodia, finger like protrusions used by cancer cells to invade into and degrade the extra-cellular matrix. Fascin, whilst normally low or absent from epithelia, localises to the leading edges of migratory cells and is over-expressed in many cancers of the same epithelial origin including lung, colorectal, pancreatic and liver. Fascin has also recently been shown to increase during inflammatory bowel disease (IBD) conditions such as diverticulitis, Crohn’s disease and ulcerative colitis. In this thesis I have investigated the role of fascin in murine models of IBD and have demonstrated that fascin is required for the haematopoietic production of leucocytes, in response to inflammation and that the loss of fascin, in the presence of high Wnt levels, results in enhanced proliferation of intestinal epithelial cells. One of the serious consequences of IBD is the increased lifetime risk of the patient developing an intestinal malignancy secondary to the disease. The exact mechanism underlying the increase in malignancies has not yet been fully established, however it is postulated that chronic inflammation and the effect this has on the major molecular pathways involved in carcinogenesis underlies the transformation from benign to malignant disease. Highest fascin expression has been shown in the dysplastic, pre-malignant cells in human IBD tissues indicating an important role of fascin in the transformation of benign to malignant cells. In this thesis, I have demonstrated that loss of fascin impairs tumour initiation in inflammatory driven and spontaneous intestinal tumourigenesis models, which is likely, in part, to be as a consequence of reduced leucocytes, in particular neutrophils, which may be CXCL2 mediated.

EHMT1 is a gene that encodes an epigenetic regulator important for normal brain development. Disruption in EHMT1 is associated with a number of neurodevelopment and psychiatric conditions, like schizophrenia, Autism Spectrum Disorders, developmental delays and intellectual disabilities. In order to help elucidate the role of Ehmt1 in cortical development two models are examined: the differentiation of mouse pyramidal neurons lacking one copy of the gene and a forebrain-specific Ehmt1-haploinsufficient mouse model. Ehmt1+/- cells demonstrated changes in cell cycle, with significant differences in proliferation rates at embryonic stem cell and neural progenitor stages. Ehmt1+/- cells demonstrated significantly different transcriptional profiles in early and late stages of progenitor development, which suggested these cells, underwent precocious differentiation. In addition, the dysregulation of mRNA expression in a number of the Nrsf/Rest repressor complex members and Rest target genes was found; and Ehmt1+/- cells did not survive as post-mitotic neurons. The forebrain-specific Ehmt1-haploinsufficient mouse model, Ehmt1D6Cre/+, importantly showed normal Mendelian birth ratios, survival, motor coordination and function and no gross morphological changes in brain structure. However, these mice demonstrated differences in activity levels and anxiety-related measurements; deficits in sensorimotor gating and object recognition; and significant differences in a number of electrophysiological measurements, including abnormal event-related neural responses in the cortex and high frequency oscillatory patterns. Taken together, these data suggest that Ehmt1 expression is important for normal pyramidal development and Ehmt1 haploinsufficiency throughout development manifests cortical dysfunction, which leads to marked behavioural and electrophysiological abnormalities.

The physicochemical nature of the infectious agent in prion diseases creates a significant challenge for decontamination services. It has been shown to be both resistant to standard methods of decontamination, used to inactivate viruses and bacteria, and to associate avidly with surgical stainless steel. Moreover, the pathophysiology of the variant, iatrogenic and sporadic forms of Creutzfeldt-Jakob Disease (CJD) suggests deposition of the infectious agent across a wide range of extraneural, lymphoid tissues, as well as in the skeletal muscle and blood. Coupled with the potential for asymptomatic carriers, there is a significant risk of iatrogenic transmission of CJD through both neurosurgical procedures and standard surgery. This PhD study was undertaken in order to improve methods of instrument decontamination and to evaluate prion detection techniques and their applicability for the assessment of prion inactivation and removal. The project has provided relevant, critical assessment of hospital decontamination procedures, in addition to guidance on how working protocols should be improved to provide a cleaner and safer end product for the patient. Moreover, laboratory studies have been performed to evaluate current methods of prion decontamination in the context of hospital procedures for instrument reprocessing. Challenges faced by sterile service departments, such as soil drying and surface degradation, have been addressed and their impact on the risk of iatrogenic transmission of prions has been investigated. Critically, the use of a fluorescent amyloid fluorophore for the detection of prionassociated amyloid as a marker for disease permitted the investigation of the role of amyloid in infectious disease under denaturing conditions. Correlation of this detection technique with the identification of PrPres by Western blot and infectious disease suggested that, whilst fluorescent detection of prion-associated amyloid was more sensitive than Western blot, PrPres detection was more specific relative to infectivity. Improved fluorophores, with greater sensitivity, have been evaluated which will enhance in situ detection of prions in the future.