Prostate cancer is the most common male cancer in the UK and USA, with a 1/13 chance of diagnosis and a 1/30 lifetime risk of death from the disease. Current treatment options include radiotherapy, surgery and hormone therapy, however 1/3 patients escape from all therapies and novel therapies are urgently required for this patient group. The University of Birmingham gene therapy group constructed two oncolytic adenovirus vectors, CRAd-NTR and vNR6, both of which contained the E1B-55K deletion and expressed the transgene nitroreductase for combined oncolytic virotherapy and enzyme/prodrug gene therapy. The latter of these two vectors, vNR6, expressing nitroreductase from the pIX virus promoter demonstrated the greatest cytotoxicity at low virus concentrations however also showed some lytic activity to non-transformed human fibroblasts. Our collaborators at the Institut Català d'Oncologia designed a panel of oncolytic adenovirus vectors with the E1A CR2 24 deletion and the E1A promoter replaced by an insulated E2F-1 promoter. The latest two in this series of vectors, termed ICOVIR-5 and ICOVIR-7, provide potential oncolytic backbones for the introduction of the therapeutic transgene nitroreductase. The aim of this thesis was therefore to ‘arm’ the ICOVIR based vectors with nitroreductase for combined oncolytic virotherapy and enzyme/prodrug therapy. At the beginning of this study no reports were published with either ICOVIR-5 or ICOVIR-7 based vectors. It was therefore first decided to construct both vectors expressing the marker transgene eGFP. These vectors were characterised in terms of cytotoxicity, transgene expression, DNA replication and E1A expression. Furthermore, these vectors were compared to the vNR3, an E1B-55K deleted virus similar to vNR6, but the eGFP ORF replacing that of pIX. The ICOVIR-7 based vectors were identified as being the most tumour selective vectors and demonstrated no cytotoxicity to non-transformed human fibroblasts, and were therefore chosen for the introduction of the therapeutic transgenes. The new ICOVIR-7 based vectors were constructed to express either wildtype, double mutant or triple mutant nitroreductase. Double and triple mutant nitroreductase are two previously characterised mutant nitroreductases, which show enhanced catalytic activity for the prodrug CB1954. The new nitroreductase expressing ICOVIR-7 vectors were characterised in terms of virus mediated cytotoxicity, tumour selectivity, E1A and NTR expression and cytotoxicity with the prodrug CB1954. One vector, expressing double mutant nitroreductase, showed the highest tumour selectivity and greatest combined cytotoxicity with the prodrug CB1954. Furthermore, this vector showed greater tumour selectivity and combined cytotoxicity than the E1B-55K deleted vector vNR6.

Epstein-Barr virus (EBV) is strongly associated with rare but aggressive lymphoproliferative diseases of NK and T cell origin. The finding of clonal and episomal forms of the virus in tumour cells from these clinically diverse diseases indicates involvement of EBV at an early stage of lymphomagenesis. However, many fundamental questions about EBV’s contribution to pathogenesis remain unanswered. In vivo analyses herein found that infection of tonsillar (but not peripheral blood) T cells occasionally occurred in primary and persistent infection, whilst infection of NK cells was a rare event. By contrast, a high EBV load was found in peripheral blood NK cells from 3 adult patients with EBV-associated haemophagocytic-lymphohistiocytosis, a disease previously associated with CD8+ T cell infection in children. Complementary studies examined EBV latent gene expression in EBV+ T/NK malignancies. Notwithstanding an apparent absence of latent membrane protein 2A and 2B (LMP2A/B), these tumour cells were recognised and killed by LMP2-specific cytotoxic T lymphocytes. This paradox was resolved by identifying a novel LMP2 mRNA, initiated from within the terminal repeat (TR) region of the viral genome and containing downstream epitope-encoding exons. Expression of LMP2-TR in T/NK cell lines and primary tissue implicates this truncated viral protein in T/NK lymphomagenesis.

B-cell specific gene PAX5 (Busslinger, 2004) is aberrantly expressed in t(8;21) AML (Tiacci et al., 2004) and is potentially involved in blocking myeloid differentiation. To understand the mechanism of PAX5 deregulation in t(8;21) AML we examined the expression, chromatin structure, histone modifications and RNA Polymerase II recruitment at PAX5 in t(8;21) AML, in non-t(8;21) myeloid precursors and in a pre-B-cell-line. Our studies show that in non t(8;21) myeloid precursors, the PAX5 gene is poised for transcription but is repressed by polycomb complexes. This polycomb repression is alleviated in t(8;21) cells leading to PAX5 expression. t(8;21) AML model Kasumi-1 carries an activating C-KIT mutation that leads to constitutive activation of different downstream signalling pathways (Larizza et al., 2005). Some of these signalling pathways have been shown to regulate association of polycomb complexes with chromatin (Voncken et al., 2005). Our study shows that small molecule mediated inhibition of constitutively activated JNK, MEK and P38 signalling in Kasumi-1 cells lead to a down regulation of PAX5 expression, decrease in elongating RNA Polymerase II and H327ac with concomitant increase in H3K27me3 at PAX5. This suggests that deregulated MAPkinase signalling in t(8;21) AML leads to the dissociation of polycomb complexes from PAX5 causing its activation. It also suggests a novel role of tyrosine kinase mutations in lineage specification and differentiation block in t(8;21) AML.

Background – Colorectal cancer (CRC) is the second most common cause of cancer death. CD4+ T cells play an important role in anti-tumour immunity by promoting immune processes that can mediate tumour inhibition. CD4+ immunity to tumours, however, is not able to prevent tumour outgrowth. It is hypothesised that tumour outgrowth can occur due to weak recognition of tumour-derived epitopes by tumour-reactive T cell receptors (TCRs) and due to negative reg-ulation by inhibitory T cell molecules. In this study, CD4+ T cell responses to the oncofoetal antigen 5T4 are studied at the molecular level. The function of the co-inhibitory molecule LAG-3 is described biophysically and monoclonal antibodies which recognise LAG-3 were devel-oped. Results – Three 5T4-reactive CD4+ T cell clones were shown to recognise 5T4-derived pep-tides restricted to HLA-DR1. Each clone was sensitive to antigen and produced TH1 cytokines despite exhibiting weak recognition of cognate antigen. Subsequently, the structural character-istics of a 5T4-derived peptide epitope was described through x-ray crystallography which revealed insights into MHC-II presentation of peptides. Cell expressed LAG-3 was shown to interact with MHC-II at the cell surface and was characterised at the protein level using surface plasmon resonance (SPR) where LAG-3 bound MHC-II via an intermediate affinity interaction. Thirdly, through the immunisation of mice, anti-LAG-3 antibodies were cloned and character-ised in terms of their specificity and function. Conclusions – These studies demonstrate how tumour-specific CD4+ T cells can produce immune-stimulatory molecules in vitro yet exhibit weak engagement of cognate antigen. It is shown that peptide flanking residues of HLA-DR1 presented epitopes can contribute to peptide anchoring as well as form structural features that may influence TCR binding. It is shown that LAG-3 binds MHC-II at higher affinity than CD4 with implications in its inhibitory function. Finally, specific antibodies that bind LAG-3 have been characterised with potential for thera-peutic development.

Dried blood spots (DBS) are drops of capillary blood collected onto filter paper from a finger prick. They have many advantages compared with traditional phlebotomy and enable patients to take samples at home. A DBS collection device was developed and incorporated into a CE marked DBS collection kit. This was successfully used in an international direct access vitamin D DBS service. A random access DBS CRP method was established for use with the DBS collection device and a new microsampling device called the Mitra. The quality of DBS received and the impact of lancet type was assessed and the effect of blood spot characteristics on CRP and vitamin D concentration was examined. The vitamin D service uptake and the population using it was analysed. The vitamin D concentration and status of users was compared to serum samples received in the laboratory from the local GP population. Significant differences between the populations were seen, with DBS users showing higher levels of vitamin D. In addition, the response to vitamin D testing for both populations was analysed. A higher rate of high to toxic vitamin D levels was seen in the blood spot population and the reasons for this were explored.

In human, cancer immunotherapeutic strategies using blocking antibodies anti-CTLA-4 and anti-PD-1 have achieved significant clinical responses. However, this has been associated with significant off target toxic autoimmune side effects that have restricted dose escalation efficacy of these therapies. Previous work in our lab generated a FoxP3K0 mouse model without FoxP3+ dependent CD4 driven autoimmunity when the TNFRSF receptors OX40 and CD30 signals are abrogated simultaneously. Thus suggests a novel approach which can be applied to abrogate off target CD4 driven side effects in cancer immunotherapy, without compromising CD8 anti-tumour immune responses. Here we showed that the CD30K0 0X40KO FoxP3K0 (tKO) mice are resistant to tumour progression in a mouse model of melanoma where anti-tumour immunity is CDS dependent. This was mimicked in CD30K0 0X40K0 (dKO) mice and WT mice treated respectively with anti-CTLA-4, anti-PD-1, or anti-CTLA-4, anti-PD-1 and anti-OX40L and anti-CD30L blocking mAbs. Interestingly, the CD4 driven autoimmunity has been abrogated using the fourfold combination: anti-(CTLA-4, PD-1. OX40L and CD30L), while an excellent CD8 anti-tumour response is preserved in C57BI/6 mice harbouring melanoma tumours. I have also investigated the effects of overexpression of IFNy in our mouse model of melanoma, using sanroque mice that show IFNy overexpression phenotype. I have shown that tumours do grow more slowly in sanroque mice. A striking finding in sanroque mice was that PD1 expression on tumour infiltrating CD4 and CD8 T cells was virtually completely abrogated, indicating that this might explain the delayed tumour growth. I found that agonistic OX40 mAbs in WT mice also downregulated PD-l expression on tumour infiltrating CD4 and CD8 T cells.

Adenovirus early region proteins, ElA, E1B-55K, E4orf3 and E4orf6 regulate host cell processes to facilitate viral replication. E4orf3 suppress host cell anti-viral activities through association with host cell proteins in E4orf3 nuclear-track structures, whilst E1B-55K, E4orf3 and E4orf6 are all recruited to viral replication centres during infection to promote viral DNA replication and inhibit host cell antiviral activities. Immunoprecipitation coupled to mass spectrometry identified Toplla as an Ad12 E4orf3-binding protein that localized with E4orf3 in adenovirus-infected cells. It was determined that Toplla expression was induced during infection, and that Toplla was required for the adenovirusdependent stabilization of p53. It was also established that, despite their ability to cooperate functionally, Toplla and p53 do not associate physically during infection. Immunoprecipitation coupled to mass spectrometry was also used to identify host cell proteins recruited to viral replication centres during adenovirus infection. The RP A-1 binding protein, Smarcall, and the FACT complex histone chaperone protein, SSRPl were identified as host cell proteins recruited to viral replication centres during infection. Following recruitment to viral replication centres Smarcall was found to be degraded in an E1B-55K and E4orf6 dependent manner, whilst SSRPl was found to be stable during infection and was not targeted for degradation.

Gastric cancer (GC), the fourth most common malignancy worldwide, has poor prognosis and treatment innovation is needed. The aims of this project were to investigate immune targets and treatment strategies for GC. I identified new T-cell epitopes in three Epstein-Barr virus (EBV) tumor antigens, LMP1, LMP2 and BARF1, expressed in the 10% of GC cases positive for EBV. T-cell clones showed that a BARF1-specific CD4 T-cell epitope restricted by HLA-DR51, an allele common in the population, was presented by an EBV-positive epithelial cancer cell line. Analysing blood and fresh tumor from newly diagnosed GC patients, I detected T-cell responses to MAGEA1, MAGEA4 and NY-ESO-1 tumour antigens in blood but not tumor. Compared to healthy donors, patients had: higher frequencies of LAG3 or CTLA4 positive CD8 T-cells, TIM-3 or CTLA4 CD4+ T-cells, T-regs, NKT-cells and gamma-delta T-cells in blood and tissue. Patients also had high granulocytic MDSC frequencies in PBMC. The CD4:CD8 ratio was low in some patients' blood, potentially indicating immunosenesence, but was always higher in tumor tissue. I successfully generated tumour infiltrating lymphocytes (TILs) from nine patients' tumors. These comprised high T-cells and NK-cells and low T-reg and MDSC. LAG-3 was increased, but PD1, was decreased on TIL T-cells. Using 3-dimensional organoids established from two patients, I showed that TIL NK-cells, but not TIL T-cells, recognized autologous tumor organoids. My results are the first proof of principle that TILs can readily be generated from gastric tumors, can target tumors cells and therefore be used to treat gastric cancer.

The investigation of human imprinting disorders has provided important insights into the role of genomic imprinting in normal health and development. Beckwith-Wiedemann syndrome (BWS) is a congenital overgrowth disorder associated with abnormal function of 11p15.5 imprinted genes that’s result, most commonly, from the epimutation (loss of maternal allele methylation) at the imprinting centre KCNQ1OT1:TSS-DMR (BWS_IC2). In contrast, Silver-Russell syndrome (SRS) is characterised by pre- and postnatal growth retardation and, most commonly, epimutations (loss of paternal allele methylation) at H19/IGF2:IG-DMR. Using Infinium 450K methylation array, I performed methylation profiling at 46 imprinted differentially methylated regions in 90 BWS and 21 SRS patients. I report epimutations at other imprinting centres outside of chromosome 11p15.5 in 40% of BWS_IC2 but not in SRS_IC1. The investigation of the potential underlying causes of this multilocus methylation disturbances (MLID) epigenotype in BWS_IC2 individuals indicated that several factors might contribute to the BWS phenotype and MLID epigenotype. Although not an universal finding, the use of assisted reproductive technology was significantly associated with MLID in my cohort of BWS_IC2 patients. Furthermore, using whole-exome sequencing strategy, I describe new potential candidate genes for trans-acting factors regulating methylation at imprinting DMRs.

Over the last two decades genetic advances have provided novel insights into the molecular basis of familial and sporadic cancers and provided the basis for the development of novel therapeutic approaches. For example, the identification of the gene for von Hippel Lindau disease provided seminal insights into its role in most clear cell renal carcinomas (RCC) and led to new treatments for RCC. In this thesis I investigated three related genetic aspects of neoplasia. Firstly, I analyzed the results of genetic testing for inherited phaeochromocytoma and investigated how clinical features could be used to stratify patients and improve the cost effectiveness of genetic testing. Secondly, I sought to identify novel causes of inherited neoplasia. Through exome sequencing of familial RCC kindreds, \(CDKN2B\) was identified as a novel familial RCC gene. The role of \(CDKN2B\) mutations in neoplasia was evaluated in familial and sporadic RCC and phaeochromocytoma. \(In\) \(vitro\) assays confirmed that germline \(CDKN2B\) mutations associated with inherited RCC caused an abrogation of tumour suppressor function. Finally, I explored how a gene-based strategy might be used to identify novel therapeutic strategies, Thus, using a siRNA library screen, in RCC cells with inactivated \(VHL\), potential candidate targets (e.g. \({PLK1/STK}\)-\(10\)) were identified for selectively decreasing the viability of RCC cells with inactivated \(VHL\).