PARV4 is a novel human parvovirus initially identified in an intravenous drug user at risk of HIV infection. PARV4 is a small single stranded DNA virus principally absent from the general population, but common in HCV- and HIV-infected individuals. Until 2009, most published PARV4 studies related to the prevalence of PARV4 in various risk groups. PARV4 has been detected in the liver of HCV-patients and the bone marrow of HIV-patients. Parvovirus B19, the closest related virus, elicits a strong immune response and can cause serious disease. Thus, this project was initiated to characterise the immune response to PARV4, and investigate the clinical significance of this virus. Cohorts of HCV-infected, HIV-infected, HCV-HIV co-infected, healthy and acute parvovirus B19-infected individuals were screened for humoral and cellular responses in both acute and chronic PARV4 infection. HCV- and HIV-related disease progression was also assessed relative to PARV4 infection. This study demonstrates that the highest prevalence of PARV4 infection is found in HCV-HIV co-infected intravenous drug users, and provides additional evidence for parenteral transmission. I present here the first data on the cellular immune response to PARV4 in acute and chronic infection and define PARV4 as a persistent virus. Although no clear correlation could be found between PARV4 and HCV or HIV disease progression, the high prevalence rates emphasize the importance of investigations into emerging infections such as PARV4.

The tumour suppressor p53 is at the centre of the signalling pathway that controls cellular processes crucial in tumourogenesis, cancer progression and tumour clearance. Alterations in the p53 pathway that lead to cancer progression can be good candidates for molecular biomarkers that would assist in the identification of patients with different prognoses, but also serve as good predictors of appropriate targeted therapies. Patient cohorts and cancer cell panels are utilised to seek associations with the attenuation of the p53 pathway and cancer progression. Firstly, the alternatively spliced transcript of the p53 inhibitor HDMX, which is frequently found in tumours with poor prognosis, is studied. The high ratio of the alternatively spliced HDMX-S transcript over the full-length HDMX-FL transcript (HDMX-S/FL) is demonstrated to associate with p53 pathway attenuation in cancer cells and breast carcinomas, and with faster metastatic progression of osteosarcoma and breast cancer patients. Secondly, inherited polymorphism in the HDMX gene is investigated and demonstrated as a unique and highly reproducible eQTL, which identifies patients with different prognoses for metastatic disease in breast cancer and melanoma cohorts. Lastly, a screening approach to identify novel inherited polymorphisms in the p53 pathway genes that associate with metastatic progression of melanoma is developed and implemented, and subsequently in silico and in vitro functional analyses are performed to investigate a mechanism behind the FOXO3 SNP, identified as the strongest candidate, whereby the experimental evidence demonstrate that the causal SNP in the FOXO3 haplotype is controlled by the GATA3 transcription factor. Together, the work presented in this thesis provides strong support for the role of the p53 pathway in the metastatic progression of cancer, and suggests that molecular biomarkers that can detect changes in the activity of p53 pathway genes could offer a robust set of biomarkers for cancer progression applicable to different types of cancer.

The skin is the site where two of the most common types of epithelial cancer, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), arise. In this work, we have investigated how ASPP2, a member of a family of proteins that interact with the p53 family, can affect skin tumourigenesis. ASPP2 is expressed in the squamous epithelia of various organs, localising exclusively in the upper and most differentiated layers. We show here that Balb/c ASPP2-null and heterozygous mice develop spontaneous SCCs. To investigate how the absence of ASPP2 from the epithelial compartment could lead to tumour formation, we analysed ASPP2’s relationship with pathways involved in the normal homeostasis of the epithelium, such as p63 and Notch. ΔNp63 is the main p63 isoform expressed in the adult epidermis, and its function is to drive the proliferation of the basal keratinocytes. Aberrant or misplaced activation of ΔNp63 in the epithelium is a known initiating cause for SCC. Consistent with this, ΔNp63 was found to be highly expressed in tumours derived from ASPP2-deficient mice. Our results indicate that ASPP2 is important in limiting ΔNp63 expression in the differentiated epithelium, preventing cell proliferation in the upper layers of the skin. This is achieved by antagonising ΔNp63 transcript and protein expression, resulting in a mutually exclusive expression pattern during differentiation of keratinocytes, as well as in epithelial cancer. ASPP2 expression was found reduced or lost in human SCC cell lines and during head and neck cancer progression, reflecting what was observed in ASPP2-deficient mice. Overall, our results indicate a possible mechanism by which p63 expression can be regulated in the skin, and provide a new model for the spontaneous formation of SCC in vivo. Additionally, we found that ASPP2 can cooperate with and enhance the activity of skin pro-differentiation pathways, such as Notch. In contrast to p63, ASPP2 and Notch1 are co-expressed in the differentiated layers of the squamous epithelium. Moreover, ASPP2 can interact with components of Notch nuclear transcriptional machinery, and it is shuttled into the nuclear compartment upon activation of Notch pathway. This recruitment results in modulation of Notch transcriptional activity on specific target genes with a differential pattern of binding sites, providing new insights into the understanding of Notch transcriptional regulation.

Multiple Endocrine Neoplasia Type 1 (MEN1) is an autosomal dominant disorder characterized by the combined occurrence of pituitary, pancreatic islet and parathyroid tumours. MEN1-associated tumours show loss of heterozygosity and the MEN1 gene encodes a putative tumour-suppressor, menin, whose over-expression in vitro inhibits cell proliferation. MEN1-associated tumours present earlier, are more aggressive and more difficult to treat than sporadic endocrine tumours. Strategies for earlier identification of index cases and novel therapies may contribute towards reduced morbidity and mortality from the condition. In this study, I first investigated the safety and efficacy of MEN1 gene replacement therapy using a modified adenoviral vector in pituitary tumours of heterozygous Men1 knockout mice. This revealed that MEN1 gene replacement was safe, effective and induced reduction of tumour cell proliferation. I also performed an in vivo phage-displayed peptide library screening study in heterozygous Men1 knockout mice to identify novel peptides that specifically bind pancreatic islet tumours. This identified one peptide sequence that likely targets pancreatic islet tumours. To further elucidate the role of menin I carried out phenotypic characterization of the mouse model for MEN1 in two mouse strains to investigate the effect of different genetic backgrounds and the potential for genetic modifiers on tumour phenotype. The frequency of pituitary and adrenal tumours was significantly influenced by the mouse strain, demonstrating the importance of genetic background on MEN1 tumour occurrence, implicating the role of genetic modifiers. Finally, I investigated the prevalence of MEN1 mutations in a cohort of patients presenting with primary hyperparathyroidism under 40 years of age. This revealed that 6% of under 40 year-olds with apparently sporadic parathyroid tumours have MEN1 mutations, and are likely to present with multiple parathyroid tumours. Pre-operative genetic screening of under 40 year-old patients with multiglandular parathyroid disease may reduce post-operative recurrence of hyperparathyroidism in those patients with MEN1 mutations.

Human Papillomaviruses (HPVs) are small DNA viruses which specifically infect keratinocytes at different body sites. An association between cutaneous Squamous Cell Carcinoma (SCC) formation, UV irradiation and infection with a high-risk subset of cutaneous HPVs has been postulated although the underlying molecular mechanisms by which HPV may play a role in SCC development are not yet fully elucidated. Expression of the viral E6 oncoprotein has been shown to interfere with DNA damage responses and inhibit UV induced apoptosis, suggesting HPV can contribute to early stages in tumourigenesis. Here, expression of E6 from HPV types 5, 8, 10, 18 and 77 was shown to reduce UV- or Fas-induced apoptosis, and the changes in a range of intracellular apoptotic regulators were investigated. Additionally, the subject of cutaneous SCCs, in contrast to HPV-associated anogenital cancers, not harboring HPV DNA in every tumor cell was explored. Results herein show that expression of E6 from skin cancer-associated HPV types 5 and 8 induced the secretion of factors that were able to inhibit UV-induced apoptosis in non-HPV expressing cell lines and primary human keratinocytes. The anti-apoptotic effect of HPV E6 expression was found to be mediated in part by upregulation of Osteoprotegerin (OPG) and Interleukin 6 (IL6). Purified OPG and IL6, when added to cells together, but not individually, reduced apoptosis following UV irradiation. Evidence is shown that OPG and IL6 inhibit the extrinsic and intrinsic apoptotic pathways respectively. Furthermore immunohistochemistry of HPV-typed SCC sections shows that IL6 protein is up-regulated in HPV positive tumors compared to HPV-negative cancers. To further test the effects of HPV5E6 expression, in combination with UV irradiation, on primary human keratinocytes microarray studies were performed. These findings support the hypothesis that a small number of HPV infected cells influence UV induced apoptosis in the skin and contribute to tumourigenesis.

Synaptic transmission in the nervous system involves the activation of receptor proteins that permit rapid transmembrane fluxes of ions. Ionic gradients across the membrane determine the direction and driving force for the flow of ions and are therefore crucial in setting the properties of synaptic transmission. These ionic gradients are established by a variety of mechanisms, including pump and transporter proteins. However, the gradients can be affected by periods of neural activity, which in turn, are predicted to influence the properties of ongoing synaptic transmission. In this thesis I have examined the concentration gradients of two ions that play a fundamental role in synaptic transmission: chloride ions (Cl-) and protons (H+). Type A γ-Aminobutyric acid receptors (GABAARs) are primarily permeable to Cl- and mediate the majority of fast post-synaptic inhibition in the brain. The transmembrane concentration gradient for Cl- is therefore a critical parameter in governing the strength of synaptic inhibition. In the first part of the Thesis I use a combination of experimental and theoretical approaches to demonstrate that influxes of Cl- via activated GABAARs can overwhelm a neurons ability to maintain a stable Cl- concentration gradient. The consequence is that subsequent activation of GABAARs results in weaker inhibition or even excitation, which alters how the neuron integrates synaptic inputs. This process is shown to be dependent upon the level of activity of the GABAAR, the post-synaptic cells membrane potential and the cellular compartment into which the Cl- flows. These principles were extended to demonstrate that popular optogenetic strategies for silencing neural activity have different effects upon GABAAR transmission. A light-activated Cl- pump was shown to cause substantial accumulations in intracellular Cl, which meant that the strength of synaptic inhibition was significantly reduced following light offset. In the second part of the Thesis I use electrophysiological and fluorescence imaging techniques to demonstrate that the activation of GABAARs during epileptiform activity results in pronounced changes to the transmembrane Cl- gradient. Indeed, these changes convert synaptic inhibition into synaptic excitation during the course of a seizure event. As part of this work I characterise a novel, genetically-encoded reporter for measuring intracellular Cl- dynamics in different cell types and subcellular compartments. A significant advantage of this reporter is that it permits the simultaneous quantification of H+ fluxes, which are also shown to change in an activity-dependent manner and which have been a confounding factor for previous Cl- reporters. In the third and final part of the Thesis I use genetically-encoded reporters to investigate activity-dependent changes in intracellular H+ concentration. I demonstrate that markedly different pH changes occur in neurons and astrocytes during epileptiform activity. Whereas neurons become acidic, astrocytes become alkaline and the dynamics of these pH shifts exhibit a very different temporal relationship with the seizure event. In conclusion, this thesis demonstrates that the intracellular concentrations of Cl- and H+ are dynamic variables that evolve across time and space, in an activity-dependent manner. Changes in the transmembrane gradients of these two ions influence ongoing synaptic transmission. Therefore this work has significant implications for our understanding of network activity and the balance of synaptic excitation and inhibition.

Neuregulin 1 (NRG1) is a growth factor implicated in neurodevelopment and postnatal maintenance of synaptic circuits. Its gene has been associated with schizophrenia, and the expression of the type I isoform (NRG1tyI) is increased in patients’ brains. Earlier behavioural phenotyping of mice over-expressing NRG1tyI revealed impairment in hippocampus-dependent spatial working memory. This present work investigates the effects of increased NRG1tyI expression on hippocampal network functioning in these mice. Fast network oscillations, specifically at gamma frequencies, were studied in CA3 hippocampal slices in a carbachol model using cellular and extracellular microelectrode recording techniques. The peak frequency of field potential oscillations was significantly reduced in slices from NRG1tyI mice compared to wild-type littermates. In addition, NRG1tyI mouse slices were more prone to develop epileptiform activity. During rhythmic activity, the balance of phasic excitation and inhibition was significantly altered in principal cells of NRG1tyI mice. Inhibitory synaptic input was more sustained, while excitatory synaptic currents were kinetically unchanged but larger and more variable in amplitude. Together, these data suggest altered functioning of the GABAergic inhibitory circuits that generate and maintain gamma oscillations. Because parvalbumin-expressing (PV+) interneurons are a major target of NRG1 signalling, the inhibition from PV+ interneurons to pyramidal cells was examined next. Channelrhodopsin-2-mediated photostimulation of PV+ cell axons failed to show changes in GABAergic inhibition of CA3 pyramidal cells in NRG1tyI mice. However, synaptic miniature glutamatergic neurotransmission was reduced in identified PV+ basket cells (BCs) and axo-axonic cells (AACs) but not in pyramidal cells. The change was expressed postsynaptically, affecting NMDA receptor- but not AMPA receptor-mediated currents. The data suggest that NRG1tyI over-expression results in alterations in PV+ interneuron types, particularly at the glutamatergic synapses that excite these cells. These changes and the altered gamma oscillations are already evident in late adolescence — before the age at which cognitive deficits are detectable.

The production of adult blood initiates from the haematopoietic stem cell (HSC). This clinically important cell has the capacity to maintain all blood lineages throughout the lifetime of an organism. HSCs emerge de novo from the haemogenic endothelium in the ventral wall of the embryonic dorsal aorta, from where they go on to seed adult sites of haematopoiesis. We have shown that Lmo4a is required for the emergence of HSCs in the zebrafish, and go on to demonstrate that Lmo4a regulates expression of the critical transcription factor, gata2a. Strikingly, both over- and under-expression of gata2a in the dorsal aorta severely diminishes HSC production. The LIM-only domain protein Lmo4 has previously been shown to interact with the known haematopoietic regulator, Ldb1. Together with our collaborators, we have identified novel binding partners of Lmo4 in mouse erythroleukaemic cells. Our functional analysis shows that many of these partners are also necessary for HSC emergence, thus revealing several new potential regulators of HSC formation. Given that these proteins were identified in an in vitro model of definitive erythropoiesis, it is remarkable that they also appear to act together in vivo at the level of HSC formation, and our data suggests that a transcriptional complex containing Lmo4 and these partners may directly repress gata2a. The related protein Lmo2 is also known to bind Ldb1. Together with Scl, Lmo2 is a master regulator of the haemangioblast programme. We have been utilising this activity, together with recent structural studies, to identify functionally important residues in the Lmo2 molecule. As a cell’s transcriptional programme drives both normal and pathological development, and misexpression of both Lmo2 and Lmo4 is involved in a variety of oncogenic states, the work presented in this thesis is likely to inform efforts to develop therapeutically relevant reagents.

The myeloid cell lineage is a fundamental element of the immune system and it can give rise to a diverse set of terminally differentiated cells, such as macrophages or osteoclasts among many others. Mutations or misregulation of gene expression may lead to severe clinical conditions, such as arthritis, osteoporosis or cancers. Epigenetics, the regulation of gene expression and chromatin remodelling, is implicated in cell differentiation, function and disease, and hence it is a promising new area to explore in order to explain underlying cellular mechanisms. Firstly, human macrophage subtypes were studied. Chemokine (C-C motif) ligand (CCL) 1 and mannose receptor were validated to be granulocyte macrophage (GM) colony stimulating factor (CSF) induced macrophage markers, while CCL₂ was specifically expressed in macrophage CSF (MCSF) macrophage population. By utilising publicly available high-throughput sequencing data, new biomarkers dehydrogenase/reductase (SDR family) member 2 and CCL₂₆ were discovered to be MCSF-macrophage specific while guanylate binding protein 5 and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A were highly up-regulated in GMCSF cells. Secondly, a range of gene knock-down techniques for the myeloid cell lineage were optimised and established. Lentiviral short-hairpin RNA (shRNA) delivery methods were shown to induce an undesirable pro-inflammatory response in macrophages. Furthermore, the frequently utilised cytomegalovirus promoter for gene expression was shown to be completely silenced in macrophage populations. Locked nucleic acids were selected as a suitable alternative to shRNA knock-down and by employing this new tool it was shown that a histone demethylase lysine (K)-specific demethylase (KDM) 6B is fundamental for macrophage differentiation. Finally, a small molecule GSK-J₄, a potent inhibitor of histone demethylases KDM6A, KDM6B and KDM₅B specific for H₃K_27me3 and H₃K_4me3, respectively, was used to dissect epigenetic signalling in osteoclasts and multiple myeloma. In osteoclasts it was shown to act mainly by inhibiting transcriptional changes required for osteoclastogenesis when MCSF-macrophages are stimulated with Receptor Activator Of Nuclear Factor Kappa-B Ligand (RANKL), as indicated by the differential increase in H₃K_27me3 marks, leading to inhibition of c-Jun and potentially abolition of transcription factor AP-1, required for the transcriptional initiation of nuclear factor of activated T-cells 1 (NFATc1). In multiple myeloma cells, GSK-J₄ causes a dramatic increase in expression, further supported by the build-up of global H₃K_4me3 marks, which results in the upregulation of the unfolded protein response pathway. In both cell systems, there is an early upregulation of metallothionein genes, which in multiple myeloma was shown to increase potentially due to rapid influx of zinc ions within the first 30 minutes, and as such may cause induction of apoptosis in multiple myeloma and may inhibit differentiation of osteoclasts.

During the course of infection with chronic pathogens such as Hepatitis C virus (HCV), Hepatitis B virus (HBV) and HIV, virus-specific CD8^+ T cells differentiate into heterogeneous dysfunctional subpopulations. Advances in multi-parameter flow cytometry have allowed these subpopulations to be further classified into classes of exhausted T cells, primarily by their expression of multiple inhibitory receptors. However, the exact phenotype of CD8^+ T cells during exhaustion is an area of great interest as many inhibitory receptors are also expressed on functional CD8^+ T cells. Discovering novel and specific markers of T cell exhaustion is fundamental in developing strategies to restore CD8^+ T cell function in chronic viral infections. Recently, genome wide expression profiles have identified broad molecular phenotypes in exhausted T cells that could not have been discovered by flow cytometry alone. I show how similar genomic approaches identify and further characterise the ectonucleotidase CD39 as a novel marker of CD8^+ T cell exhaustion in chronic viral infection. I show that CD39 is highly expressed in HCV and HIV-specific CD8^+ T cells and that CD39^+ CD8^+ T cells are enriched with gene signatures of exhaustion. CD39 is highly co-expressed with multiple inhibitory receptors including PD-1, enzymatically active on CD8^+ T cells in HCV infection and positively correlated with viral load in both HCV and HIV. I also demonstrate the discovery of a novel CD39^High population of cells in the mouse model of chronic Lymphocytic Choriomenigitis Virus (LCMV) infection, which express the highest degrees of PD-1, LAG3 and 2B4 in the CD39^+ fraction. Thus, CD39 is a novel and specific marker of severe CD8^+ T cell exhaustion in human and animal models of chronic viral infection.