Sir Peter MacCallum Department of Oncology - Theses
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ItemNo Preview AvailableDevelopment of new methods for accurate estimation of tumour heterogeneity( 2022)It is now understood that intra-tumor heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure and one of the main reasons for poor overall survival in cancer patients. However, the possibility to study this phenomenon is so far underexplored as the acquisition of multi region data sets from the different tumour sites can be ethically challenging. With circulating tumour DNA (ctDNA) used as a proxy for tumour biopsies, it is possible to analyse a snapshot of the unified heterogeneity in each patient, but there is still an unmet need for new methods to optimize the analysis of these large-scale, high-dimensional data to derive new treatment targets. The contributions of this work include the development of multiple new methods, which show that the analysis of bulk sequencing from tumour tissue and ctDNA has unrealised potential for both diagnostic and research questions. This thesis presents three distinct but related projects, which explore the analysis of tumour heterogeneity at different levels and depths, focusing on method development. First, we developed a workflow to improve the detection of somatic variants present at very low allele frequencies. When multiple samples, separated in time or space, from the same patient were available, we were able to substantially improve the detection threshold of variants. These low abundance variants are invaluable in a clinical setting, where they can indicate an arising resistance mechanism or relapse of disease. With the improved sensitivity of our method, the treatment of patients can be adjusted earlier and more accurately. We then used our new analysis workflows to explore evolutionary trajectories and resistance pathways of five lung cancer patients enrolled in the CASCADE autopsy program. In addition to analysis of somatic variants, we used copy number analysis and structural variants to contrast and compare each sample within a patient to generate phylogenies to visualise the evolutionary distances and a pseudo time scale to assess the timing of mutations. Clear genomic determinants of treatment resistance were identified for three of the five cases with non-small cell lung cancer and the diversity of these genomic mechanisms profoundly highlighted the true extent of inter-patient heterogeneity. This work included the identification of a novel genomic resistance mechanism to the drug selpercatinib, a small molecule inhibitor of REK kinase. Among the remaining two patients, treatment resistance was mediated by transformation of their disease from non-small cell lung cancer to a small cell lung cancer histological phenotype. These two cases showed distinct evolutionary trajectories compared to the other non-small cell lung cancer cases, with similarity in their nuclear and mitochondrial phylogenies, but no clear genetic determinant for the small cell transformation, highlighting the additional importance of non-genomic mechanisms which can drive resistance in this disease. Finally, we developed a method, called MisMatchFinder, to monitor tumour heterogeneity and evolution over time through ctDNA. We tailored the method to be fully tumour agnostic and enabled it to be easily applied in the clinical setting by using low-coverage whole genome sequencing. The method uses highly specialised filtering steps to enrich the tumour signal and eliminate the background noise from normal cell-free DNA and sequencing errors in these data. We showed that the method could accurately detect specific cancer-related signatures at low tumour purity and tumour burden in simulated and patient data for melanoma and breast cancer. In summary, with this work we contributed multiple new methods to study, measure and understand genetic tumour heterogeneity. This understanding is crucial for the continuous optimisation of cancer management and the development of new and effective treatments for patients.
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ItemAntimicrobials in hospitalised and high-risk children: understanding and improving use( 2021)Infection is a near-universal human experience and is responsible for substantial child mortality across the globe, despite impressive reductions in child mortality and morbidity since the twentieth century. Antibiotics and other antimicrobial drugs have transformed our ability to prevent and treat infection. In general, these drugs are so safe, effective and widely available that overuse and inappropriate use are common. This is a cause of real problems in hospitals and the community, with unintended consequences of antimicrobial use including rising antimicrobial resistance. Antimicrobial stewardship (AMS) is aimed at improving the safety and efficacy of prescribing and has received growing attention in recent years. However, evidence to support and improve AMS for Australian children in hospitals is lacking. Australian hospitals are mandated to implement AMS programs and provide access to appropriate national and/or local prescribing guidelines. However, hospitals are under no current obligation to provide appropriately targeted AMS for the children in their care. Prior to mid-2019, national antimicrobial guidelines contained little paediatric and no neonatal advice. Since 2013, the voluntary National Antimicrobial Prescribing Survey (NAPS) has provided national reports on prescribing. However, until now, paediatric-specific data have not been reported. Compared with the literature on adult AMS, research on paediatric AMS is lacking, with few high-quality studies on interventions to improve care. This situation creates challenges for child healthcare providers and paediatric AMS program leaders, and more evidence is required to prioritise and improve care. The overall aims of this thesis are to improve the understanding of current antimicrobial use and stewardship for children in Australian hospitals and determine priorities to improve antimicrobial use now and in the future. This is achieved by analysing antimicrobial prescribing epidemiology and quality using national datasets, including national point prevalence survey and cohort study data. Chapter 1 reviews antimicrobial prescribing to children in hospitals, including in Australia. Chapter 2 presents the first analysis of paediatric antimicrobial prescribing to children in hospitals throughout Australia using NAPS data. Chapter 3 turns to high-risk groups, presenting the first nationwide analysis of prescribing for neonatal sepsis and fungal infections, again using NAPS data. Chapter 4 presents an analysis of antimicrobial prescribing in a contemporary cohort of immunocompromised children with fever and neutropenia, including prescribing quality and outcomes. Chapter 5 presents an interventional study evaluating the implementation of Australian guidelines on antibiotic duration and intravenous-to-oral switch. This is an example of the evidence translation and implementation approach needed for sustainable AMS improvement. Chapter 6 concludes the thesis, discussing the implications of the research and the paediatric AMS horizon in Australia. The analyses reported here reveal unnecessary variations in care and systemic inequities, which have implications for policy and guidelines. Non-metropolitan and non-tertiary hospitals in general provide lower-quality antimicrobial prescribing to children. This is likely to reflect decreased access to high-quality AMS resources, including guidelines and personnel, suggesting the need for systemic improvements. Neonates in Australian hospitals receive highly structured care in terms of antimicrobial choice and indications, but variations in dosing are substantial and undesirable, reflecting the lack of use of national guidelines. Prescribing for febrile neutropenia is highly diverse and often includes empiric aminoglycosides, which this research reveals are associated with real harm, suggesting the need for national guidelines to optimise care. Finally, the standard management of infections in hospitals involves excessive intravenous therapy, which is associated with unnecessarily increased hospital length of stay. As demonstrated, this can be improved with a structured AMS program, which should be available wherever children are treated in hospital. The information generated by this thesis provides new evidence on current antimicrobial prescribing practice and priorities and demonstrates the importance of utilising routinely collected data for the surveillance and improvement of paediatric AMS. Since this body of research began, national guidelines and paediatric-specific resources are now being developed, establishing new benchmarks. Along with continuous surveillance, these must be implemented appropriately to improve care. The research collaborations and networks developed during the production of this thesis will be used to support future surveillance and implementation work, which is needed to address AMS priorities in Australia and support the research and development of paediatric AMS across the globe.
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ItemThe control of lymphatic vascular remodelling in cancer by microRNAs( 2021)Metastasis is the lethal aspect of cancer for most patients. Remodelling of lymphatic vessels associated with a tumour is a key initial step in metastasis because it facilitates the entry of cancer cells into the lymphatic vasculature and their spread to lymph nodes and distant organs. Although it is clear that vascular endothelial growth factors (VEGFs), such as VEGFC and VEGFD, are key drivers of lymphatic remodelling in cancer, the means by which many signalling pathways in endothelial cells are co-ordinately regulated to drive growth and remodelling of lymphatics in cancer is not understood. In this thesis, I seek to understand the broader molecular mechanisms that control cancer metastasis through the analysis of microRNAs which act to co-ordinately regulate signalling pathways involved in complex biological responses, such as lymphatic remodelling, in health and disease. Here, using high-throughput small RNA sequencing, I found that a specific microRNA, miR-132, is up-regulated in expression in lymphatic endothelial cells (LECs) in response to stimulation with VEGFC and VEGFD. Interestingly, inhibiting the effects of miR-132 in LECs in vitro blocked proliferation and tube formation of these cells induced by VEGFC and VEGFD - LEC proliferation and tube formation are key steps in lymphatic remodelling. Moreover, I demonstrated that miR-132 is expressed in the lymphatic vessels of a subset of human breast tumours which were previously found to express high levels of VEGFD. In order to dissect the complexity of molecular regulation by miR-132 in lymphatic biology, my collaborators and I identified miR-132 target mRNAs in LECs, using high-throughput sequencing after RNA-protein cross-linking and immunoprecipitation of the Argonaute protein (Argonaute HITS-CLIP), which led us to define the miR-132-mRNA interactome in LECs. We found that this microRNA in LECs is involved in the control of many different molecular pathways mainly involved in cell proliferation and regulation of the extracellular matrix and cell-cell junctions. It is logical that miR-132 regulates such pathways given they are involved in the processes of LEC proliferation and tube formation, which I showed are dependent on miR-132 in my in vitro studies. Finally, I demonstrated that inhibiting the effects of miR-132 in a mouse ear model of lymphangiogenesis, using an antagomiR inhibitor of miR-132 coupled to cholesterol, blocked the complex remodelling of lymphatic vessels stimulated by VEGFC, in vivo. It was noteworthy that all aspects of lymphatic remodelling induced by VEGFC were restricted by inhibition of miR-132, including the enlargement, branching and sprouting of lymphatic vessels. Thus the inhibitory effect of targeting this microRNA on lymphangiogenesis and lymphatic remodelling can be considered comprehensive. The research described in this thesis identified miR-132 as a critical regulator of lymphangiogenesis and lymphatic remodelling, and delineated molecular mechanisms by which this microRNA influences these important biological processes. This work also identified new molecular pathways which are involved in modifying the lymphatic vasculature in response to key lymphangiogenic growth factors. In-so-doing, these studies identified potential therapeutic targets for drugs designed to block the growth and remodelling of tumour lymphatics, and thereby restrict the metastatic spread of cancer.
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ItemPan-cancer reconstruction of clonal evolution in 1,800 patients using the discrete time-branching process( 2020)Intra and inter-tumour heterogeneity poses a challenge for associating molecular and immunohistochemical markers with clinical outcomes. Sequencing technologies has enabled detailed assessment of tumour heterogeneity, facilitating the genomic characterisation of tumours. Whilst such technologies have revealed mutational landscapes and have identified key driver alterations for tumorigenesis, pan-cancer clonal evolution reconstructions are lacking. In order to bridge this gap, I used discrete-time branching models to derive biological insights into tumour progression and reconstructed the clonal evolution in 1,800 patients, successfully linking mutations with growth patterns of disease progression. I first modified a discrete time-branching process to account for individual clonal subpopulations and derived analytical solutions for expectation and variance of both clonal and tumour expansions. Additionally, I derived the expected time for any given clone to successfully expand as \hat{\tau}, and with the use of these analytical solutions, I showed the likely driver and clonal compositions of the tumours and their phylogenies. Secondly, I generated a database of results from four different versions of time-branching process models that covered multiple parameters. Here I identified how an increase in diversity arises by both increased mutation rate and reduced fitness. I further corroborated that total number of drug resistant cells is directly proportional to lineage extinction probability (\delta) and tumour size as shown in previous studies. I also showed that this effect can be extrapolated to other types of functional passenger mutations involved in cancer-specific mortality. Moreover, I showed how commonly used sequencing cut-offs limit the accurate inference of tumour’s average selective advantage and driver mutation rate. Thirdly, I identified that a minimum distance metric can provide accurate fits of simulated cancer cell fractions to real patient tumour data. This metric showed at least 80% accuracy to identify the initial parameters of s and u and at least 40% accuracy to recover the correct evolutionary trajectory. Fourthly, I applied this fitting procedure to reconstruct the evolutionary trajectories of 1,800 tumours from different cancer sequencing studies. The best fits derived suggests that the most likely parameters for the evolution of solid tumours are high driver mutation rates and weak driver effects of fitness. Fifthly, using The Cancer Genome Atlas cohort, I identified an association between predicted degree of clonality and survival, and found branched topologies are common in malignancies with adverse prognosis. In the TRACERx non-small-cell lung cancer cohort, I identified that clonal reconstructions agreed with previously reported phylogenies. Additionally, using data from the Breast International Group 1-98, I identified the role of tumour fitness in determining clinical outcome, and the evolutionary dynamics of TP53 and PIK3CA mutations conducive to distant metastasis. Finally, using data from a metastatic melanoma patient collected through the CASCADE melanoma study, I was able to propose a pattern of dissemination from the primary to metastatic sites in the liver and brain based on the phylogenies recovered from my data-fitting procedure. This study demonstrates the power of the discrete-time branching process in reconstructing tumour evolution, and its potential to uncover insights in the dynamics of tumour growth that are missed by current methods.
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ItemDefining functional drivers of oesophageal tumourigenesis( 2019)The incidence of oesophageal adenocarcinoma (OAC) has risen rapidly over the last four decades and has a high overall mortality rate that has shown only incremental improvements over the same duration. OAC develops from the precursor intestinal metaplasia of the oesophageal mucosa known as Barrett’s oesophagus. However, limited knowledge of the molecular mechanisms driving disease progression makes effective clinical management of OAC challenging. One of the common genetic events associated with the progression from Barrett’s oesophagus to OAC is loss of the tumour suppressor, SMAD4 (mutated in 13% or loss of function in 34% of OAC cases). Herein, this thesis firstly investigated the effect of SMAD4 inactivation in Barrett’s carcinogenesis. Genetic knockdown or knockout of SMAD4 was sufficient to initiate tumourigenesis of dysplastic Barrett’s oesophagus cell line, CP-B, in vivo, establishing SMAD4 loss as a crucial event driving progression to OAC. Further, low coverage whole genome sequencing (LC-WGS) analysis revealed that tumourigenic SMAD4 knockdown/knockout CP-B cell lines exhibited distinctive and consistent copy number alterations (CNAs) compared to non-tumourigenic SMAD4 wild-type parental cells. Amongst the alterations we observed were loss of chromosome arm 14q, while amplified regions include chromosome arms 6q and 12p, consistent with common CNAs found in patient tumours. This high genomic instability, characterized by structural chromosomal rearrangements within the tumours following SMAD4 loss, implicates SMAD4 as a protector of genome integrity in OAC development and progression. Moreover, initial in vitro data shows that SMAD4 knockout in CP-B cell line, results in differential expression of transforming growth factor-beta (TGF-beta) pathway target genes (such as ACTA2, CRYAB, PTK2B, ATF3 and CDC6) and loss of cell cycle arrest in response to TGF-beta1 cytokine compared to SMAD4 wild-type parental cells. Furthermore, SMAD4 knockout negatively regulated transcript expression of the multifunctional tumour suppressor INK4/ARF locus, demonstrating the novel and complex network of SMAD4 tumour suppressive activity. This thesis also focused on deciphering the functional role of growth factor receptor bound protein 7 (GRB7) amplification and overexpression in OAC and its potential targeting. GRB7 gene is positioned within known 17q12 amplicon, together with HER2 gene encoding for human epidermal growth factor receptor 2 (HER2). GRB7 is an adaptor molecule that mediates networking of multiple cell surface receptors with downstream signalling pathways. GRB7 high expression was found to be associated with worse survival in OAC patient cohort. Further, genetic GRB7 knockdown (siRNA) inhibited cell proliferation and clonogenic survival and induced apoptosis in GRB7 amplified and overexpressing OAC cell lines (OE19 and Eso26), without altering proliferation of the cells with normal GRB7 expression. Furthermore, whilst HER2 amplification and overexpression was also observed in OE19 and Eso26 cells, they were not uniquely sensitive to trastuzumab (HER2 inhibitor), with Eso26 cells exhibiting resistance in vitro. Taken together, initial findings raise the possibility that GRB7 may be a better molecular therapeutic target than HER2 in OAC with the 17q12 amplicon. To address this possibility, OE19 and Eso26 cell line xenograft models with inducible expression of shRNA targeting GRB7 were used. Consistent with in vitro findings, HER2 expression did not predict sensitivity to trastuzumab, with Eso26 xenografts remaining refractory to trastuzumab treatment. Of high importance, mimicking GRB7 inhibition with inducible-shRNA significantly inhibited tumour growth in both OE19 and Eso26 xenografts. Thus, this part of the thesis demonstrates the functional role of GRB7 overexpression as an oncogenic driver independent of HER2. In summary, the identification of functional genetic drivers and a deeper understanding of the mechanisms that underlie tumour progression in Barrett’s carcinogenesis will lead to improved strategies for the clinical management of OAC patients. To this end, SMAD4 loss was sufficient for progression from dysplasia to OAC. Tumours driven by SMAD4 loss exhibit distinctive CNAs consistent with OAC and metastatic potential. In addition, GRB7 high expression predicts poor outcome in patients with OAC and as such, GRB7 represents an oncogenic driver that could be used as a therapeutic target. Crucially, this thesis provides in vitro and in vivo preclinical and molecular biology evidence for the potential therapeutic benefit of targeting GRB7 in cancer.
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ItemExploration of novel regulators of mutant p53 in cancer cells: a role for NDFIP1( 2019)Mutations in the tumour suppressor gene, TP53 occur in more than 50% of human cancers. Mutant p53 proteins not only lose their tumour suppressive capacities, but also gain oncogenic functions, broadly referred to as gain of function (GOF). Cancer cells frequently accumulate mutant p53 and may become addicted to this protein for their survival. During development, mutant p53, like its wild-type counterpart, is inherently labile, however in cancer cells mutant p53 frequently accumulates. In part, this is due to the interrupted auto-regulatory loop with MDM2. However, MDM2 alone cannot explain the stability of mutant p53 in many cancer contexts. We therefore argued that additional factors are responsible for its stability in cancer cells. In order to identify the major players in the regulation of mutant p53, we performed a high-throughput RNAi screen through which we evaluated 18,120 genes for their effects on mutant p53 levels in two different mutant p53 expressing cell lines. Based on network analyses, pathway analyses and extensive literature mining, we selected 37 candidate genes to be validated through p53 immunoblotting. From the validated genes, we have selected one candidate for further studies. The results described in this thesis highlight a previously unknown mode of mutant p53 regulation in cancer cells. Future studies will explore in greater depth the functional consequences of this new interaction with mutant p53. Excitingly, these studies expose new vulnerabilities for therapeutic intervention and these opportunities for targeting aggressive cancers with mutant p53 will also be the focus of ongoing research.
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ItemThe evolutionary history of genes and transcriptional networks reveals fundamental properties of cancer associated with the breakdown of multicellularity( 2018)All biological systems follow the rules and constraints imposed during their evolution. Current-day gene phenotypes such as gene expression, gene essentiality, gene function and protein localization are linked with the time of evolutionary emergence of genes. In cancer, tumours rely on cellular processes that date back to unicellular ancestors (e.g., cell replication, glycolysis), while dysregulating key pathways linked to the emergence of multicellularity, suggesting that the transition from unicellularity to multicellularity left vulnerabilities in cells that act as guiding principles during cancer development. Therefore, in this thesis I integrate genomics, systems biology and evolutionary biology to investigate fundamental principles of tumourigenesis related to the evolutionary history of genes using gene expression and somatic mutation information across multiple tumour types. First, I coupled the evolutionary age of genes and cellular processes with their expression levels in tumour and normal samples, and found that tumours consistently activate genes from unicellular ancestors while switching off genes related to multicellularity. These consistent patterns were supported by a mutual exclusivity between the activity of genes and transcriptional networks of unicellular and multicellular ancestors, which promoted convergent evolution towards a state of loss of multicellularity. Second, I investigated how somatic mutations disrupted gene regulatory networks. Genes that emerged together with early metazoans were enriched in point mutations and copy- number alterations, indicating that gene innovations that took place at the onset of multicellularity play a fundamental role in cancer development. Importantly, the uncoupling of regulatory networks of unicellular and multicellular ancestors was mostly due to point mutations in gene regulators linking these networks. On the other hand, copy-number aberrations were directly involved in the activation and inactivation of unicellular and multicellular genes, suggesting point mutations and copy-number aberrations play complementary roles in the loss of regulation between unicellular and multicellular transcriptional networks in cancer. Third, I focused on novel transcriptional associations formed during tumourigenesis using gene co-expression module analysis. Significant levels of rewiring between unicellular and multicellular genes were found across tumours. This rewiring was mostly driven by gene amplifications, which promoted the formation of tumour-specific modules composed of novel transcriptional associations between unicellular and multicellular genes, once more linking the genes and regulatory associations evolved at the onset of multicellularity to cancer development. The findings of this work reveal fundamental principles driving cancer development associated with genes and transcriptional networks evolved during the transition from unicellularity to multicellularity. I propose a model whereby activation of programs that date back to unicellular ancestors and the deactivation of multicellular programs is driven by an inherent mutual exclusivity of these genes together with the breakage of regulation between unicellular and multicellular genes by point mutations, whereas the formation of novel transcriptional associations between these genes in tumours is driven by copy-number changes. Finally, I identify potential novel drivers based on their key role in uncoupling unicellular and multicellular transcriptional networks across tumours and suggest novel treatment strategies derived from this evolutionary approach. The results presented in this thesis contribute to our understanding of how past evolutionary events led to vulnerabilities in transcriptional networks that influence cancer development, and highlight the benefits of the integration of evolutionary concepts with genomics and network biology to identify fundamental principles of cancer.
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ItemHow information technology improves the quality and efficiency of medical care and research( 2018)In 2007, the concept of rapid learning healthcare was proposed in the United States of America health system in a response to increasing healthcare costs. Its aim was to accelerate knowledge discovery through a systematic approach to integrating electronic medical records design with analysis infrastructure to rapidly and continuously assess health system performance. The delivery of healthcare is becoming increasingly performed and documented within the electronic domain, and large databases of healthcare-related information being created as a by-product. This has led to an unprecedented level of access to detailed and structured clinical data that could be used to accelerate research. In a rapid learning healthcare system, the high level of integration from electronic record to policy would ensure that each patient and each click of the mouse would drive innovation. The attraction of rapid learning was not to supplant the traditional clinical trial paradigm, but to augment its effectiveness with accelerated analysis of real-world outcomes. The rapid learning concept relied heavily on electronic medical records, administrative systems and disease registries as data sources to power analyses. Electronic health record penetrance in Australia has lagged that achieved in the USA, primarily because of financial assistance provided as part of the HITECH act in the USA. However, one exception is seen in oncology, where radiotherapy is exclusively prescribed electronically. Additionally, there has been a significant shift toward electronic chemotherapy prescribing due to the clinical risk associated with manual systems. Perhaps in oncology there is an opportunity to replicate the successes of data-driven health research achieved elsewhere. The objective of the work contained in this thesis is to develop practical methods to expand and discover the infrastructure required to implement rapid learning health care in the Australian oncology context. Ultimately, the aim is to increase the quality and efficiency of medical care and research by harnessing novel information technology (IT) methods. In addition to leveraging existing secondary databases for health services research and creating high impact linkages with state-level cancer registries, advanced IT methods could also be used to automate manual data extraction tasks in a timely and cost-effective fashion. The integration of these methods into routine clinical practice has enormous implications for tracking patient care quality, and accelerating research by utilising all data by-products of health care.
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ItemInvestigating acquired resistance to Pol I transcription inhibitors for the treatment of haematologic malignancies( 2018)Previous work from our group and others has demonstrated that CX-5461 (Senhwa Biosciences), a first-in-class small molecule inhibitor of RNA Polymerase I transcription of the ribosomal RNA genes, is effective at treating a range of different cancers both in vitro and in vivo, and is currently in clinical trials for haematologic and solid tumours. However, despite initial tumour clearance in response to CX-5461 treatment in preclinical murine models of cancer, mice eventually relapse with tumours that are resistant to further CX-5461 treatment. This thesis investigates the mechanisms via which the tumours can develop resistance to CX-5461 treatment and extrapolates this research to better understand: 1) how CX-5461 functions as an anti-tumour agent; 2) which pathways are required to mediate resistance to CX-5461; and 3) how resistance can be overcome with combination therapy. Using DNA exome sequencing, we found that Top2α is frequently mutated in tumours that have acquired resistance to CX-5461 treatment in vivo. Functional characterization of a Top2α mutant cell line demonstrated that Top2α expression and activity were reduced in these cells. Indeed, we found that knockdown of Top2α was sufficient to cause resistance to CX-5461. This implies that Top2α could provide a novel biomarker for CX-5461 response in clinical trials. Further investigation of the CX-5461 resistance mechanism uncovered that CX-5461 also acts as a Top2 inhibitor in addition to its ability to inhibit rDNA transcription. However, unlike common chemotherapeutic Top2 inhibitors which kill cells by causing genome-wide DNA damage thereby initiating a DNA damage response, CX-5461 treatment causes comparatively fewer DNA breaks enriched at the ribosomal DNA promoter loci. Thus, CX-5461 is able to kill tumour cells via the DNA damage response in the absence of extensive DNA damage thereby potentially limiting the cytotoxicity of drug treatment. Together, the work presented in this thesis identifies novel mechanisms of action and resistance to CX-5461. We propose that CX-5461 and other second-generation inhibitors of RNA Polymerase I and Top2α may provide a viable, less genotoxic alternative to classic Top2 inhibitors.
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ItemFever and neutropenia in children with cancer: optimising clinical research and the delivery of care in Australia( 2017)Fever and neutropenia (FN) is the most common complication of childhood cancer treatment. Management traditionally involves hospital admission for antibiotics until resolution of fever and recovery of neutrophil count. However, children with FN are a heterogeneous group with varying risk of severe infection, and this approach over treats up to half of all episodes where risk of serious complications is low. Unlike FN management for adults, formal low-risk treatment strategies for children are not routinely employed. In Australia, little is known about the aetiology and management of FN in children and clinical decision rules (CDRs), designed to predict infection, have not been validated. These factors remain a critical barrier to implementing ambulatory-care programs for children with low-risk FN in this country. Such programs are safe, improve quality of life (QoL) and reduce healthcare expenditures. The overall aims of this thesis were to optimise clinical paediatric FN research; to advance our understanding of the assessment and management of FN in children with cancer in Australia; and to facilitate treatment that is tailored to the patient’s risk of infection. Each project addresses important evidence gaps, namely the absence of standardised paediatric FN research outcomes and definitions, the lack of a contemporary evaluation of FN management in Australia and the limited use of risk-based treatment algorithms. To optimise clinical paediatric FN research, Delphi survey methodology was used to achieve consensus on a set of core variables and outcomes that should be reported in all FN studies. This is the first time a paediatric-specific FN research framework has been developed and is the result of an international collaboration. Standardised FN research outcomes will reduce heterogeneity between studies, minimise reporting bias and enable research results to be compared, contrasted and combined. To advance our understanding of the management of FN in Australia, a national practice survey was conducted. There was clear evidence of heterogeneity in assessment, risk stratification and treatment of children with FN. The survey identified critical knowledge gaps and deviations from best practice, and the results will be used to inform guidelines, education and low-risk program implementation strategies. It also highlighted the necessity for validation studies to determine which CDRs are most appropriate for use in Australia. A series of studies were conducted to facilitate FN treatment that is tailored to the risk of infection. In a retrospective study, seven CDRs were validated, of which two exhibited the most clinically meaningful results. The accompanying economic evaluation highlights opportunities for substantial healthcare savings by reducing length of stay (LOS) for low-risk patients. The systematic review and meta-analysis of the predictive ability of novel biomarkers found that marked heterogeneity between studies limits firm conclusions, and further research is required. This thesis has addressed key evidence gaps and contributed new knowledge that will optimise clinical FN research and the delivery of FN care to children with cancer. It has informed the national Australian Predicting Infectious ComplicatioNs in Children with Cancer (PICNICC) project that will prospectively validate CDRs, identify novel biomarkers and evaluate the cost and QoL associated with standard FN treatment. It has also established a collaborative network that will ensure FN research continues in this country and results are translated into practice.