The Mater Medical Research Institute proposes to undertake a Phase I clinical trial using CMRF-56 immunoselected blood dendritic cells (BDC) loaded with control and myeloma-associated tumour peptide antigens for the treatment of multiple myeloma (MM) patients with minimal residual disease. This thesis describes some of the fundamental pre-clinical in vitro experiments undertaken in preparation for this trial so as to maximise the potential of this vaccine to induce myeloma-specific immune responses. These experiments involved determining the parameters for optimal activation of the CMRF-56 immunoselected cell preparation and exploring the potential of novel myeloma peptide antigens to induce anti-myeloma cytotoxic T lymphocyte (CTL) responses. CMRF-56 immunoselected cell preparations, containing predominately myeloid BDC, monocytes and B cells, were prepared from both healthy donors and myeloma patients. Activation of this preparation with granulocyte macrophage colony stimulating factor (GM-CSF) was found to increase co-stimulatory molecule expression by and survival of BDC, improve peptide- and lysate-specific CTL induction, and, in combination with prostaglandin E2 (PGE2), improve chemokine-specific migration of BDC. Following optimisation of in vitro CTL generation protocols, GM-CSF activated CMRF-56 immunoselected cells were examined for their ability to induce myeloma-specific immunity. Using lysate from myeloma cell line U266 as an antigen source, a polyclonal T cell pool was generated within which peptide specific CTL recognising myeloma antigens Muc1, HM1.24/BST2, DKK-1 and CT-7/MAGE-C1 could be identified. Furthermore, GM-CSF activated CMRF-56 immunoselected cells pulsed with HLA-A*201 restricted peptides derived from Muc1, HM1.24/BST2 and CT-7/MAGE-C1 could induce CTL capable of lysing both peptide- and myeloma cell line targets in both healthy donors and myeloma patients. These results provide the first evidence of immunogenic HLA-A*201 restricted epitopes of novel myeloma antigen CT-7/MAGE-C1. The data collected in this study supports the application of GM-CSF activated CMRF-56 immunoselected cells loaded with defined myeloma peptide antigens for the therapeutic vaccination of MM patients with minimal residual disease.

[Truncated abstract] A paradox exists in tumour immunology whereby progressive tumour growth exists in parallel with an anti-tumour T cell response. This defective T cell response is thought to result from the induction of T cell tolerance and/or tumour induced immunosuppression, which act to inhibit the activation, differentiation and function of tumour-specific CD8+ T cells. Dendritic cells (DCs) are professional antigen presenting cells (APCs) that are critical to the generation of effective CTL; however their function and phenotype is often defective or altered in tumour-bearing hosts, which may limit their capacity to mount an effective tumour specific T cell response. In this thesis, the role of DCs in the cross-presentation of tumour antigen was assessed in terms of their APC function, migration and location. In doing so the intention was to gain insight into the early processes that potentially contribute to the development of an ineffective anti-tumour immune response. This study examined cross-presentation of the nominal tumour antigen, influenza A hemagglutinin (HA) expressed by the murine malignant mesothelioma cell line, AB1-HA. Cross-presentation was predominantly restricted to the local draining lymph nodes throughout tumour growth and was mediated by CD8a+ and CD8a- DCs. This results in an ineffective CTL response due to the lack of DC activation and the presence of potentially immunosuppressive B7 molecules. However, the capacity of the CD8a- DC subset to cross-present antigen suggested a role for migratory tumour-resident DCs in this process. Analysis of tumour infiltrating DCs showed that they were paralysed in their capacity to cross-present tumour antigen and were immobilised at the tumour site. Conversely, cross-presentation of tumour antigen in the local draining lymph node was dependent on the continuous traffic of antigen from the tumour microenvironment. In this vein, small numbers of metastatic tumour cells were detected in the draining lymph nodes, however their isolation was dependent on the removal of DCs and T cells, suggesting immune control of metastatic spread. Thus, tumour cells may be the source of antigen for cross-presentation by DCs in the tumour draining lymph nodes. .... In conclusion, the results presented in this thesis support a role for DCs in the generation of tumour-specific T cell responses that fail to control tumour growth. In addition the results provide a basis for further investigation into the effects of chemotherapy on the source and form of tumour antigen for cross-presentation by specific DC subsets in the tumour bearing host. These findings may have important implications for the development of future anti-cancer immune therapies targeting DCs.

The Mater Medical Research Institute proposes to undertake a Phase I clinical trial using CMRF-56 immunoselected blood dendritic cells (BDC) loaded with control and myeloma-associated tumour peptide antigens for the treatment of multiple myeloma (MM) patients with minimal residual disease. This thesis describes some of the fundamental pre-clinical in vitro experiments undertaken in preparation for this trial so as to maximise the potential of this vaccine to induce myeloma-specific immune responses. These experiments involved determining the parameters for optimal activation of the CMRF-56 immunoselected cell preparation and exploring the potential of novel myeloma peptide antigens to induce anti-myeloma cytotoxic T lymphocyte (CTL) responses. CMRF-56 immunoselected cell preparations, containing predominately myeloid BDC, monocytes and B cells, were prepared from both healthy donors and myeloma patients. Activation of this preparation with granulocyte macrophage colony stimulating factor (GM-CSF) was found to increase co-stimulatory molecule expression by and survival of BDC, improve peptide- and lysate-specific CTL induction, and, in combination with prostaglandin E2 (PGE2), improve chemokine-specific migration of BDC. Following optimisation of in vitro CTL generation protocols, GM-CSF activated CMRF-56 immunoselected cells were examined for their ability to induce myeloma-specific immunity. Using lysate from myeloma cell line U266 as an antigen source, a polyclonal T cell pool was generated within which peptide specific CTL recognising myeloma antigens Muc1, HM1.24/BST2, DKK-1 and CT-7/MAGE-C1 could be identified. Furthermore, GM-CSF activated CMRF-56 immunoselected cells pulsed with HLA-A*201 restricted peptides derived from Muc1, HM1.24/BST2 and CT-7/MAGE-C1 could induce CTL capable of lysing both peptide- and myeloma cell line targets in both healthy donors and myeloma patients. These results provide the first evidence of immunogenic HLA-A*201 restricted epitopes of novel myeloma antigen CT-7/MAGE-C1. The data collected in this study supports the application of GM-CSF activated CMRF-56 immunoselected cells loaded with defined myeloma peptide antigens for the therapeutic vaccination of MM patients with minimal residual disease.

Four tumour active trinuclear complexes: DH4Cl: [{trans-PtCl(NH3)2}2m-{trans-Pd( NH3)2(H2N(CH2)4NH2)2]Cl4, DH5Cl: [{trans-PtCl(NH3)2}2m-{trans-Pd( NH3)2(H2N(CH2)5NH2)2]Cl4, DH6Cl: [{trans-PtCl(NH3)2}2m-{trans-Pd( NH3)2(H2N(CH2)6NH2)2]Cl4, DH7Cl: [{trans-PtCl(NH3)2}2m-{trans-Pd(NH3)2-( H2N(CH2)7NH2)2]Cl4 and one dinuclear complex DHD: [{trans-PtCl(NH3)2}�-{ H2N(CH2)6NH2}{trans-PdCl(NH3)2]Cl(NO3), have been prepared and characterised based on elemental analyses, IR, Raman, mass and 1 H NMR spectral measurements. For the trinuclear complexes, the synthesis has been carried out using a step-up method branching out from the central palladium unit. A purity of about 95% has been obtained by repeated dissolution and precipitation. The activity against human cancer cell lines including ovary cell lines: A2780, A2780 cisR , A2780 ZD0473R , non small lung cell line: NCI-H640 and melanoma: Me-10538 have been determined based on MMT assay. Cell uptakes, DNA-binding have been determined for ovary cell lines: A2780, A2780 cisR . The nature of interaction with pBR322 plasmid DNA and ssDNA has been studied for trinuclear complexes DH4Cl, DH5Cl, DH6Cl and DH7Cl and the dinuclear complex DHD. Interaction of DH6Cl with adenine and guanine has also been studied by HPLC. The compounds are found to exhibit significant anticancer activity against cancer cell lines especially ovarian cancer cell lines: A2780, A2780 cisR and A2780 ZD0473R . DH6Cl in which the linking diamine has six carbon atoms is found to be the most active compound. As the number of carbon atoms in thelinking diamine is changed from the optimum value of six, the activity is found to decrease, illustrating the structure-activity relationship. The increase in uptake of the trinuclear complexes in A2780 cell line with the increase in size of the linking diamine coupled with the low molar conductivity values found for the solutions of the compounds suggest that the compounds would remain in solution as undissociated �molecules� and hence could cross the cell membrane by passive diffusion. Much lower resistance factors for the all the multinuclear compounds including DHD as applied to A2780 cisR cell line, as compared to that for cisplatin, suggest that the compounds are able to overcome multiple mechanisms of resistance operating in the cell line. All of the multinuclear complexes are expected to form long-range interstrand GG adducts with DNA, causing irreversible global changes in the DNA conformation but unlike cisplatin do not cause sufficient DNA bending to be recognized by HMG 1 protein. Increasing prevention of BamH1 digestion with the increase in concentration of the multinuclear compounds also provide support to the idea that the compounds because of the formation of a plethora of interstrand GG adducts are able to cause irreversible changes in DNA conformation. The results of the study show that indeed new trinuclear tumour active compounds can be found by replacing the central platinum unit in BBR3464 with other suitable metal units.

The typical response of cancer patients to treatment is only temporary, and is often followed by relapse. The failure of various therapeutic strategies is commonly attributed to the emergence of drug resistance. The response patterns for patients under such treatments indicate that complex dynamics regulate the response of the tumour to the therapy. The environment in which the tumour lives (the stroma) is known to be a modulator of multiple mechanisms that lead to drug resistance and seems to be a likely candidate for explaining some of this complexity. Understanding the role of stromal cells in the promotion of drug resistance is critical for the design of optimal treatment strategies, and for the development of novel therapies that selectively target both the tumour and the stroma. In this thesis we design two novel mathematical models that describe cancer growth within its environment and the evolution of drug resistance within spatially complex and temporally dynamic tumours. A compartment model captures clinically observed dynamics and allows direct comparison with experimental data, facilitating model parametrisation and the understanding of inter-tumour heterogeneity. An individual cell-based model highlights the key role of local interactions, determining heterogeneity at the tissue scale, that will eventually determine treatment outcome. A non-spatial approximation of this second model allows us to find analytic guidelines for the design of effective therapy. These tools allow the simulation of a range of treatment strategies (including combination of different drugs and variation of schedule) as well as the investigation of therapy response based on patient- or organ-specic parameters. The work developed in this dissertation is based on the paradigmatic biology of melanoma and non-small cell lung cancer. Its results are therefore applicable to a variety of cancer treatments that target similar processes, and whose therapeutic failure can be attributed to environment-mediated drug resistance.

Acute myeloid leukaemia (AML) and ovarian cancer (OVC) are two difficult to treat cancers. AML is often treatable however minimal residual disease (MRD) endures such that many patients who achieve remission eventually relapse and succumb to the disease. OVC affects approximately 7000 women in the U.K. every year. It can occur at any age but is most common after menopause. Diagnosis at an early stage of disease greatly improves the chances of survival however, patients tend to be diagnosed in the later stages of disease when treatment is often less effective. Immunotherapy has the potential to reduce MRD and delay or prevent relapse. In order for immunotherapy to work, tumour antigens need to be identified and characterised so they can be effectively targeted. Personalised treatments require the identification of biomarkers, for disease detection and confirmation, as well as to provide an indication of best treatment and the prediction of survival. PASD1 has been found to be frequently expressed in haematological malignancies and I wanted to determine if there was a correlation between the presence of antigen-specific T cells in the periphery of patients with AML and PASD1 protein expression in the leukaemic cells. The expression of other leukaemia antigens were concurrently examined as comparators. I performed RT-PCR on nine antigens and immunocytochemistry on PASD1 in 18 samples from AML patients. I found a correlation between PASD1 expression in AML samples and the presence of PASD1-specific T cells as detected on the pMHC array. OVC lacks suitable targets for immunotherapy with few CTAs having been identified. I examined the expression of SSX2IP and the CTAs PASD1 and SSX2 in OVC. I compared the protein expression of these known tumour antigens to the “gold standard” biomarker for the diagnosis of OVC, CA125 and two other proteins known to be promising in the diagnosis of OVC, HE4 and WT1. I analysed commercially available paraffin-embedded OVC multiple tissue arrays (MTAs) containing 191 samples, predominantly stage I (n= 166), II (n= 15) and III (n= 6) OVC as well as healthy donor (n= 8) and normal adjacent tissues (n= 8). Scoring was performed in a single blinded fashion. I found SSX2A to be expressed at a score level of 3 with a frequency (37/191) that exceeded that of CA125 (14/191), HE4 (14/191), WT1 (1//191) or PASD1 (0/191). To confirm this expression I used two additional commercially-available antibodies that recognise the region common to SSX2A and B, and an antibody specific for SSX2A. Using SSX2 peptides, I blocked the immunolabelling of SSX2 in SSX2-positive cell lines showing that the immunolabelling of SSX2 and SSX2A was specific. I demonstrated that the expression of SSX2 and specifically SSX2A was reproducible and restricted to ovarian cancer with little or no expression in endometrial tissues, or diseased or inflamed endometrial tissue. In summary, these studies demonstrated that PASD1 expression in leukaemia cells correlated with the presence of PASD1-specific T cells in the periphery of presentation AML patients. I have shown that PASD1 specific-T cells are present in AML patients at diagnosis and that immunotherapy targeting PASD1 could be used to break tolerance and clear residual leukaemia cells during first remission. Analysis of the expression of three antigens in OVC, identified the specific expression of SSX2, in particular SSX2A in OVC but not healthy or diseased endometrial tissues. The expression of SSX2A was more frequent and more specific to OVC, than HE4 and WT1, and more frequent at higher intensity, especially in early stage OVC, than CA125. SSX2 and explicitly SSX2A requires further investigation to determine whether the high level of background at score 2 can be reduced with better blocking of non-specific sites. This may require the use of different SSX2 antibodies or an improved staining protocol.

RNA interference (RNAi) is a natural mechanism of cellular defence against exogenous double stranded RNA (dsRNA). The discovery of small dsRNA molecules which can be processed by the RNAi pathway in mammalian cells was one of the key advances in the study of functional genomics. These molecules can be designed to downregulate the expression of specific genes. Collections or libraries of dsRNA molecules targeting an extensive number of genes are now available. Using these libraries, numerous studies have implemented high-throughput screens for the study of molecular effectors of numerous phenotypes. The process of designing an RNAi screen requires the consideration of several critical factors during both the experimental and analysis phases. The experimental screen should aim to reproduce the biological phenomenon studied as closely as possible by choosing an adequate model and screening conditions. Phenotype evaluation and assessment of knockdown effects need careful consideration. The results obtained from large-scale RNAi screens are often complex. An analysis pipeline should be implemented which integrates the biological basis of the phenomenon and facilitates the interpretation of the data. This project designed and implemented an unbiased shRNA screen in two in vitro models relevant to carcinogenesis and diabetes. The first screen implemented used a model of neighbour suppression to study the molecular effectors of the response in tumorigenic cells to growth suppression cues from the surrounding tissue, a cellular interaction relevant in early tumorigenesis. The second screen studied two phenotypes relevant to diabetes: proliferation and resistance to lipotoxicity of β-cells in a reversibly immortalised  cell line. An integrative analysis pipeline was also developed to apply network biology and functional enrichment analysis methods for the interpretation of the data obtained from both screens.

Background: Brain tumour is a disease that can affect the life of the patient, both physically and mentally. Relatives to the patient of brain tumor lives with an uncertainty about how the disease will develop and affect their loved one, which leads to a dramatic change of their everyday life. Method: A qualitative, manifest content analysis with an inductive approach based on biographies. Aim: The aim of this study is to describe women’s experiences of living with a brain tumor. Findings: The result showed that the female patients experienced suffering in living with a brain tumor since they were affected both physically and mentally. To feel dependent on others and to not identify with who you had become, was strong signs on their changed everyday life. Even though these women experienced suffering they could feel hope and gain strength from their surroundings and their relatives. Conclusion: Women that live with brain tumor narrates experiences of difficult changes but also feelings of well-being during the entire course of the disease. These women experienced well-being whenever they accepted the disease, when they got support from their relatives and whenever their feelings where confirmed by the professional carers. All of these aspects contributed to these women’s well-being. / Bakgrund: Hjärntumör är en sjukdom som kan medföra en livsförändring hos patienten med både psykiska och fysiska förändringar. Närstående till de som är drabbade av hjärntumör lever med en stor ovisshet kring hur sjukdomen kan utveckla sig och påverka den sjuka vilket leder till en kamp i deras förändrade vardag. Metod: En kvalitativ, manifest innehållsanalys med en induktiv ansats utifrån självbiografier. Syfte: Syftet är att beskriva kvinnors upplevelser av att leva med en hjärntumör. Resultat: Resultatet visade att kvinnorna upplevde stora motgångar av att leva med hjärntumör då dess konsekvenser tedde sig i både fysiska och kognitiva svikter. Att uppleva ett beroende av andra och att inte längre vara sig lik var starka tecken på de kvinnliga patienternas förändrade vardag. Trots motgångarna upplevde kvinnorna en hoppfullhet och fann kraft i sin omgivning. De närstående till kvinnorna hade en stor betydelse för dem. Slutsats: Studien påvisar att kvinnor som är drabbade av hjärntumör skildrar upplevelser av svåra förändringar men även av välbefinnande under sin sjukdomsperiod. Acceptansen av sjukdomen samt närståendes stöd och vårdens bekräftelse är faktorer som bidrar till välbefinnande trots hjärntumören.

Complex network models of functional connectivity have emerged as a paradigm shift in brain mapping over the past decade. Despite significant attention within the neuroimaging and cognitive neuroscience communities, these approaches have hitherto not been extensively explored in neurosurgery. The aim of this thesis is to investigate how the field of connectomics can contribute to understanding the effects of focal brain lesions and to functional brain mapping in neurosurgery. This datasets for this thesis include a clinical population with focal brain tumours and a cohort focused on healthy adolescent brain development. Multiple network analyses of increasing complexity are performed based upon resting state functional MRI. In patients with focal brain tumours, the full complement of resting state networks were apparent, while also suggesting putative patterns of network plasticity. Connectome analysis was able to identify potential signatures of node robustness and connections at risk that could be used to individually plan surgery. Focal lesions induced the formation of new hubs while down regulating previously established hubs. Overall these data are consistent with a dynamic rather than a static response to the presence of focal lesions. Adolescent brain development demonstrated discrete dynamics with distinct gender specific and age-gender interactions. Network architecture also became more robust, particularly to random removal of nodes and edges. Overall these data provide evidence for the early vulnerability rather than enhanced plasticity of brain networks. In summary, this thesis presents a combined analysis of pathological and healthy development datasets focused on understanding the functional effects of focal brain lesions at a network level. The coda serves as an introduction to a forthcoming study, known as Connectomics and Electrical Stimulation for Augmenting Resection (CAESAR), which is an evolution of the results and methods herein.

Understanding the mechanisms and nature of tumour heterogeneity is a key focus of current cancer research. Tumour heterogeneity can arise from clonal evolution and/or differentiation. This thesis investigated the role of methylation in dynamic regulation of CD24 based heterogeneity in colorectal cancer cell lines. First, E-Cadherin variation between the cell lines LS174T and LS180 was investigated to find out whether E-Cadherin had any causal role in the difference in lumen formation between these two cell lines derived from the same tumour. These studies found no evidence of a causal role of E-Cadherin. However, morphological heterogeneity in LS174T was observed during the E-Cadherin study, suggesting that this cell line might be a mixture of two different clones. Single cell sorting by FACS allowed to isolate and establish these clones which were stable in the culture for long enough (until passage ~30) to allow their characterisations. Between the two clones, the CD24⁺ clone (named the LS174T_Clone 1^CD24+) was found to have shorter doubling time (23 hours) than the CD24- clone (named the LS174T_Clone 2CD24-; 30 hours). When cultured in matrigel, the LS174T_Clone 1^CD24+ showed higher clonogenicity (Chapter 4). Microarray analysis further revealed differences in gene expression including LAPTM4B, CXCR4, TGFIB and IL8 between these clones. Interestingly, when maintained for a long time in culture (around passage 50, which is equivalent to ~7 months), CD24 expression went through a gradual change in these clones, which became more evident from subclones of LS174T_Clone 2^CD24- (Chapter 6) and clones from another CRC cell line SW480 (chapter 5 and 6). To understand the mechanism of this dynamic change in the expression of CD24, it was first shown that no mutation could be responsible for this phenomenon. This suggested that promoter methylation of CD24 might be the mechanism of the observed dynamic changes in CD24 expression. Bisulfite (BS) modification of DNA from the LS174T clones and CD24 differentially expressing CRC cell lines (such as CD24- cell lines: CC20, RKO vs CD24+ cell lines: DLD1, NCIH716) followed by Sanger sequencing showed that direct methylation of seven CpG positions in the CD24 promoter region Chr6:106975560-106975834 is strongly correlated with the expression of CD24. Further subcloning and sequencing revealed that changes in the methylation of only two out of the seven CpG positions might be the main contributor to the CD24 expression differences. This is the first evidence of direct methylation-mediated regulation of CD24, showing, more broadly, how methylation can contribute to and maintain dynamic heterogeneity in cancer cells. Finally, a mixed culture experiment with the CD24+ and CD24- clones was conducted to test a simple mathematical model, which aimed to explain the interaction between the clones that are stably present in the LS174T cell line (Chapter 7). Altogether, these experiments suggest that genes such as REG1A (an inducer of angiogenesis) might be expressed because of synergistic interactions between the clones, whereas CXCR4 and TFF2 might be involved in a receptor-ligand complementary relationship. These findings have set a ground for future studies to confirm such interactions between co-existing subpopulations within a heterogeneous milieu of cancer cells.