Sir Peter MacCallum Department of Oncology - Theses

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    The role of lysine acetyl transferases and epigenetic regulators in T-cell mediated anti-tumour immune-responses
    Pijpers, Lizzy Maria Gertruda ( 2023-09)
    Adoptive cell therapy using chimeric antigen receptor (CAR) T cells has demonstrated remarkable success in treating haematological malignancies, resulting in the FDA approval of six CAR T cell products for the treatment of B cell Acute Lymphoblastic Leukaemia, multiple myeloma and non-Hodgkin lymphoma. However, CAR T cells have shown limited efficacy against solid tumours in the clinic, which is primarily attributed to the immunosuppressive nature of the tumour microenvironment and antigen heterogeneity of solid tumours. Hence, strategies to overcome these challenges are necessary for CAR T cells to be effective in solid malignancies. Improved clinical outcomes have been associated with CAR T cells exhibiting memory T cell characteristics. While the transcriptional control of memory differentiation is extensively studied, our understanding of the epigenetic mechanisms underlying these gene expression changes have yet to be fully understood. In this thesis, primary human and mouse (CAR) T cells were utilized to study the epigenetic landscape of CD8+ T cell activation and differentiation. A485, a novel histone acetyltransferase inhibitor of P300 and CBP was discovered in a small molecule compound screen to regulate memory T cell differentiation. Treatment of T cells with A485 resulted in memory phenotype differentiation with the corresponding transcriptional changes: upregulation of T cell memory associated genes and downregulation of T cell effector associated genes. In vivo data across various mice tumour models, collectively demonstrated the potent anti-tumour effect of pre-treating (CAR) T cells with A485 prior to adoptive transfer. Given that the P300 and CBP histone acetyltransferase inhibitor A485 was found to regulate memory T cell differentiation, the role of histone acetylation in T cell activation and differentiation was investigated. Histone acetylation was found to be rapidly enhanced upon T cell activation. In addition, P300 and CBP mediated histone acetylation was found to be critical for memory T cell differentiation in the time prior to first T cell division at 24 to 48 hours post activation. H3K27ac ChIP data suggest that P300 and CBP might preferentially acetylate effector-associated super enhancers at 2 hours post T cell activation, thus leading to memory T cell differentiation upon A485 inhibition. Although, P300 and CBP are often described as an entity, this thesis, proposes potential independent roles, with CBP involved in regulating memory T cell differentiation. Overall, the results presented in this thesis improve our understanding of the role of histone acetylation in T cell activation and differentiation.
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    Uncovering epigenetic regulators of bivalent MHC class I genes in cancer
    Sparbier, Christina ( 2023-06)
    Recent breakthroughs in cancer immunotherapy have transformed the management of many malignancies and renewed interest in the molecular understanding of tumour antigen presentation. However, despite the success of these therapies, resistance remains a significant challenge for many patients. One prominent resistance mechanism involves the disruption of major histocompatibility complex class I (MHC-I) antigen presentation, which has been demonstrated to occur through inactivating mutations or transcriptional silencing in the MHC-I antigen presentation pathway, with the latter presenting as a potentially reversible and, therefore, targetable mechanism of resistance. In this thesis, I investigate the epigenetic mechanisms underlying MHC-I resistance in cancer. Firstly, I elucidate the significance of the polycomb repressive complex 2 (PRC2) in maintaining transcriptional repression of MHC-I, which is conserved across different species, including humans, mice, and Tasmanian devils. The silencing of MHC-I by PRC2 in cancer cells facilitates the evasion of T-cell killing. However, I demonstrate that this can be overcome through genetic or pharmacological depletion of PRC2. By conducting ChIP-sequencing, I identify that silenced MHC-I genes in cancer cells exhibit bivalent modifications, specifically repressive H3K27me3 and activating H3K4me3 marks, which is a developmental process seen in embryonic stem cells and maintained during neural progenitor differentiation. Collectively, these findings reveal how cancer cells can co-opt an evolutionarily conserved, lineage-specific function of PRC2 to silence MHC-I antigen presentation and evade immune surveillance. Driven by the observation that bivalency is often dysregulated in cancer, I set out to identify the regulators of bivalent chromatin. Building upon the previous observation that MHC-I is bivalently modified, I leveraged this characteristic as a readout and conducted whole genome CRISPR/Cas9 screens to pinpoint key regulators involved. I uncover specific roles of the PRC2.1 and PRC1.1 sub-complexes in maintaining silencing of bivalent gene expression. Unexpectedly, I make the intriguing discovery that genetic depletion or pharmacological inhibition of Menin, traditionally known as a co-activator and a component of the KMT2A/B H3K4me3 methyltransferase complexes, phenocopies the effects of polycomb disruption. This results in the derepression of bivalent genes in cancer and human pluripotent and embryonic stem cells, findings which challenge the existing paradigm whereby disruption of the KMT2A/B and polycomb complexes is expected to have opposing effects on bivalent gene regulation. Furthermore, my research reveals an essential role of KMT2A/B in MHC-I gene expression following Menin inhibition and, therefore, highlights the existence of Menin-independent and Menin-dependent functions of KMT2A/B. Finally, I demonstrate that targeting the Menin-KMT2A interaction leads to the release and redistribution of KMT2A from active genes to bivalent genes, which creates a permissive chromatin environment that facilitates gene activation. My research has uncovered previously unknown roles for specific components of the KMT2A/B and polycomb complexes in regulating bivalency. Moreover, these findings have significant implications for cancer therapy. By identifying strategies to overcome transcriptional MHC-I repression, my work provides a compelling rationale for utilising inhibitors targeting PRC2 and Menin in the treatment of difficult-to-treat malignancies. Additionally, these insights offer potential avenues for developing novel therapeutic approaches to effectively treat cancers characterised by low MHC-I expression.
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    Study of the immunomodulatory effects of radiation therapy in solid cancers
    Sia, Joseph Ikin ( 2020)
    Radiation therapy (RT) has evolved over more than a century into a well-established, highly sophisticated and major cancer treatment modality today. A paradigm shift that has occurred within the last two decades is the growing understanding that RT can induce host immune responses that contribute to tumour control, beyond direct radiation-induced cytotoxicity. Contemporaneously, the advent of modern cancer immunotherapy such as immune checkpoint inhibitors has revolutionised the field of oncology and highlighted the potential of harnessing the immune system to suppress and eradicate tumours. Inevitably, resistance to cancer immunotherapy has also brought into focus immunological barriers that preclude cancer immunity. In this context, an increasing body of pre-clinical and clinical studies substantiate the use of RT as a unique candidate to complement cancer immunotherapy in non-overlapping mechanisms to overcome such barriers. However, instruction on the optimal integration of RT and cancer immunotherapy is scarce. For the radiation oncologist, an outstanding gap in knowledge is how radiation dose-fractionation influences the immunomodulatory effects of RT and its synergy with cancer immunotherapy. In this PhD project, mouse models of solid cancer were used to systematically interrogate this question by employing a series of rationally selected radiation dose-fractionation regimens to dissect the immunological impact of dose per fraction (DPF) from that of total dose, as represented by biological effective dose (BED). In orthotopic AT3-OVA mammary carcinomas, radiation-induced CD8+ T cell responses were found to be regulated by radiation DPF, rather than BED. By contrast, radiation-induced natural killer (NK) cell responses in the same tumours were independent of radiation DPF but required a sufficient BED. Mechanistic investigations examining the cellular and transcriptional changes in AT3-OVA tumours evoked by radiation demonstrated that the differential regulation of anti-tumour immune responses by radiation DPF and BED was not primarily dictated by differences in tumour cell-intrinsic immunogenicity, but rather by the effector and suppressor dynamics in the tumour immune microenvironment, of which regulatory T cells played a central role. Furthermore, cross-examination of subcutaneously implanted MC38 colon carcinomas and publicly available transcriptomic data of human cancers pre- and post-RT suggested that radiation-induced immune responses are also significantly shaped by the tumour type. Lastly, the impact of radiation dose-fractionation on the anti-tumour activity of immune checkpoint inhibitors targeting the adaptive and innate immune arms was examined in AT3-OVA tumours, confirming the corollary that RT and immune checkpoint inhibitors do not universally synergise, but require selection of radiation regimens and checkpoint targets that are predicated on biological rationale. Overall, this PhD project represents a comprehensive side-by-side pre-clinical study of the effects of radiation dose-fractionation on host anti-tumour immune responses. Results presented herein contribute towards a clearer understanding of this complex and clinically urgent question. More broadly, insights from this project will help guide the refashioning of RT into an exciting key adjunct in the immuno-oncology era.
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    Targeting the tumour microenvironment to enhance immunotherapy against cancer
    Oliver, Amanda Jane ( 2020)
    Cancer immunotherapies have shown astounding clinical results within the last decade, with complete eradication of advanced malignancies in certain cancer types, particularly melanoma and non-small cell lung cancer (NSCLC). These successes lead to clinical approval in multiple countries for checkpoint blockade and chimeric antigen receptor (CAR) T cell therapies, and the award of the 2018 Nobel Prize in Physiology or Medicine to James P. Allison and Tasuku Honjo for their research on checkpoint blockade molecules. Despite this, many patients receive minimal benefit and focus has shifted to understanding how to predict and enhance immunotherapy responses. It is now well established that the tumour microenvironment (TME) is a major limiting factor for immunotherapy efficacy. Studies in mice using genetically identical tumour lines implanted in different tissues have demonstrated that the location of tumour growth can directly impact the composition of the TME and response to anti-cancer therapies. Retrospective analysis of checkpoint blockade treated patients’ revealed tissue-specific patterns of response, where metastases in certain anatomical sites were more responsive than others. To date studies investigating the tissue-specific influence on immunotherapy responses in vivo have limited clinical relevance, and studies in patients are minimal. In this thesis, we investigated the influence of the tissue-specific TME on immunotherapy responses in vivo and assessed tissue-specific patterns in the TME of breast cancer metastases from patient samples. First, we investigated a murine breast cancer model comparing responses of primary tumours to tumours in the liver and lungs as common metastatic sites to two immunotherapies, anti-PD-1/anti-CTLA4 and trimAb (anti-4-1BB, anti-CD40, anti-DR5). We reported that the 67NR tumour line growing in the lungs was resistant to immunotherapy, whereas the same tumour line growing in the mammary fat pad (MFP, primary tumour site) or liver could be completely eradicated in a portion of mice. Our analysis revealed that the resistance of lung tumours was independent of the tumour cells, vasculature or drug delivery and that the immune TMEs of lung and MFP tumours were distinct. Specifically, we demonstrated that lung tumours had a more immunosuppressive TME, with increased myeloid derived suppressor cells (MDSCs), decreased T cells and decreased activation of T cells and natural killer (NK) cells. Furthermore, upon depletion of various immune subsets alongside therapeutic intervention we found that NK cell depletion had a significant impact on lung tumours, but not MFP tumours. Taken together our data suggests that tumours grown in different tissues sculpt different TMEs with varied levels of immunosuppression and require different immune cell subsets, and perhaps different immune stimulants, for optimal anti-tumour responses. Following on from this study, we next wanted to assess responses to immunotherapy in vivo in models where multiple tumours in different anatomical sites were present. The rationale of this model was to investigate a more accurate representation of advanced cancer, where tumours have metastasised to multiple locations throughout the body. We hypothesised that co-existing tumours in different sites with disparate TMEs could influence immunotherapy responses compared to tumours existing alone. Our results indicated that the presence of a concomitant MFP tumour enhanced responses of lung tumours to trimAb or anti-PD-1/anti-CTLA4 therapies compared with mice bearing only lung tumours. We observed a decrease in lung metastasis burden in mice with simultaneous MFP tumour growth even before therapy commencement, which likely contributed to enhanced therapy responses. Upon interrogation we found that CD8+ T cells were responsible for the decrease in lung tumour burden and that the lungs of mice with co-existing MPF tumours had more tumour reactive CD8+ T cells. From our results, we hypothesised that the presence of a tumour in a more immunogenic location, such as the MFP, promoted T cell priming within the tumour draining lymph node (TdLN) at this site and led to a systemic response against distal tumours, such as tumours within the lungs. Lastly, we aimed to identify tissue-specific patterns within metastases from human tumours. Herein, we utilised metastatic tumour samples collected as part of the cancer tissue collection after death (CASCADE) rapid autopsy program from three estrogen receptor positive (ER+) breast cancer patients and one triple negative breast cancer (TNBC) patient. We analysed the immune profiles of these samples by transcriptomic and immunohistochemical (IHC) analyses. Our data demonstrated that, although there were potential tissue-specific differences within the TME, the most significant trend delineated immunological differences between ER+ and TNBC patients. These results confirmed previous research describing a higher immune infiltrate in TNBC samples compared with ER+ samples. Our research highlights the potential of investigating metastatic tumour samples however, future studies with separation of disease subtypes and increased sample sizes are needed to truly investigate tissue-specific patterns within the TME. In summary, the data presented in this thesis highlights the importance in further defining tissue-specific response patterns and mechanisms in patients to optimise current and future immunotherapies. Our results indicate that an in depth understanding of the tissue-specific TME could reveal novel treatment options in tumours that are non-responsive to current immunotherapies.
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    Investigating the mechanism of cytotoxic lymphocyte resistance to perforin
    Rudd-Schmidt, Jesse Alexander ( 2020)
    Cytotoxic lymphocytes are highly efficient killer cells of the immune system. They destroy cognate target cells by secreting highly toxic effector molecules, the pore-forming protein perforin and pro-apoptotic serine proteases granzymes, into the confines of the immune synapse. Despite both the lymphocyte and target cell plasma membrane being equally exposed to the perforin and granzymes, the lymphocytes invariably survive that encounter as they remain resistant to perforin pores. This project investigates the mechanisms behind this unique phenomenon.