Paediatrics (RCH) - Theses
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ItemMicroRNA expression and genome-wide epigenetic analysis of paediatric acute myeloid leukaemia( 2014)Introduction: Paediatric Acute Myeloid Leukaemia (AML) is the third most prevalent cancer in Australian children under the age of 14. Chromosomal and genetic lesions are commonly found within specific subtypes of paediatric AML and these help to direct treatments and prognostic predictions. However, there are no common genetic lesions across subtypes of paediatric AML and subtype-associated genetic changes may fail to induce leukaemogenesis. DNA methylation is the most commonly studied molecular alteration in cancer. Strong evidence indicates that methylation variations exist within paediatric cancer known to modify gene expression. Similarly, microRNA are small non-coding RNA that also regulate gene expression and whose dysregulation within paediatric cancer is now beginning to be appreciated. Therefore altered methylation and miRNA expression may contribute to malignancy through activating oncogenes or inactivating tumour suppressor genes, similar to genetic mutations. Furthermore, both DNA methylation and microRNA expression represent viable epigenetic mechanisms for application to clinical biomarkers of disease diagnosis, prognosis and disease tracking. At the beginning of this study, limited interrogations of genome-scale DNA methylation and microRNA expression had been conducted within paediatric AML with appropriate non-leukaemic controls. Furthermore, there has been few extensive studies evaluating the utility of current epigenetic techniques on primary clinical specimens. Therefore I chose to study genome-wide DNA methylation and large-scale miRNA expression changes in paediatric AML, as well as interrogating techniques for using archived primary patient samples. Materials and Methods: Two approaches were used to interrogate large-scale DNA methylation and microRNA expression; TaqMan OpenArray Human MicroRNA Panel (Life Technologies) was used to interrogate 5 primary paediatric AML patients with matched controls; and Illumina Infinium HumanMethylation450 BeadChip array (HM450) was used to interrogate 18 primary AML alongside matched non-leukaemic samples. Validation of AML DNA methylation alterations was conducted using the SEQUENOM MassARRAY EpiTYPER with an expanded cohort of 28 patients, in conjunction with validation of microRNA expression utilising quantitative real-time PCR (qRT-PCR) and TaqMan singleplex assays on 32 primary paediatric AML, together with matched control groups. This study also developed extensive extraction techniques for the analysis of microRNA expression within a range of samples, including archived bone marrow aspirate smear slides. Results: Genome-scale DNA methylation disruptions were characterised within paediatric AML, and identified hundreds of genes associated with disease compared to matched control samples. Interrogation of a refined subset of target genes also identified gene expression alterations within these regions, which were further associated with patient disease onset and predicted outcome. Conversely, large-scale microRNA expression disruptions were characterised within paediatric AML, whereby a small number of reliable targets were identified. Such microRNA disruption was found to be associated with DNA methylation regulation on the microRNA gene, and could also be used as reliable biomarkers to predict disease onset and patient outcome in connection with identified patient cytogenetic abnormalities. Integration of data from genome-scale DNA methylation and combined gene and microRNA expression analysis, identified common epigenetic disruptions within paediatric AML affecting known tumour suppressor genes, cytoskeletal organisation, cellular proliferation and immune function. Conclusions: The findings of this study reveal that DNA methylation alterations within paediatric AML can associate with gene disruptions with the potential to initiate and perpetuate malignant phenotypes. Likewise, microRNA deregulation can establish widespread gene disruptions as a catalyst for leukaemogenesis. Interestingly we establish that combined deregulation of epigenetic mechanisms, and the occurrence of one epigenetic mechanism working to deregulate another, may be a common feature of paediatric AML. Lastly this study identifies targets and techniques to extend such studies into the clinic and provides attractive targets for therapeutic intervention.
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ItemDNA methylation patterns in paediatric acute lymphoblastic leukaemia( 2014)Introduction: Disruption of DNA methylation is the most common molecular alteration in human cancers. Paediatric Acute Lymphoblastic Leukaemia (ALL) is the most prevalent childhood cancer and strong evidence indicates that DNA methylation alterations exist within this disease. Several genetic mutations have been described that contribute to the malignant transformation within the B-cell subtypes of ALL (B-ALL), however many of the malignant phenotypes are unexplained by genetic mutations alone. DNA methylation has the ability to alter gene expression and thus DNA methylation alterations may contribute to observed malignant phenotypes, potentially activating oncogenes or inactivating tumour suppressor genes analogous to genetic mutations. Furthermore, DNA methylation alterations represent viable clinical biomarkers for disease diagnosis, prognosis and disease tracking. At the start of this project, preliminary genome-scale DNA methylation profiling had been performed on paediatric B-ALL with appropriate B-cell controls to identify contributing DNA methylation alterations and only limited studies had investigated techniques, thresholds and assays for the clinical implementation of DNA methylation biomarkers. Materials and Methods: Two approaches were used to characterise genome-scale DNA methylation alterations in 69 paediatric B-ALL patients; the Illumina Infinium HumanMethylation BeadChip arrays HM27 and HM450. Validation of B-ALL DNA methylation alterations was conducted using the SEQUENOM MassARRAY EpiTYPER. Genome-scale analysis of gene expression (Affymetrix microarray) was also performed in 17 B-ALL cases and integrated with B-ALL methylome data. The study also developed novel techniques for the analysis of DNA methylation using MALDI-TOF Mass Spectrometry (SEQUENOM). Results: Genome-scale disruptions in DNA methylation were characterised in paediatric B-ALL, validating a number of previous small scale experiments and identifying hundreds of genes with associated DNA methylation disruption. DNA methylation alterations were found to be prevalent in all paediatric B-ALL subtypes and stable biomarkers of disease. Two highly differentially methylated sites in the gene promoters of FOXE3 and TLX3 were used as targets to establish new MALDI-TOF Mass Spectrometry techniques that could 1) analyse multiple DNA methylation regions in single reaction and 2) sensitively detect rare DNA methylation events. The techniques were applied to patient samples and enabled high sensitivity and specificity measurements for disease diagnosis. Furthermore, these techniques enabled sensitive disease tracking and insights into the detection of minimal residual disease by DNA methylation analysis. Integration of genome-scale DNA methylation and gene expression data identified common and subtype-specific epigenetic disruption in paediatric B-ALL effecting known tumour suppressors and genes implicated in apoptosis, cellular proliferation and cell signalling. Furthermore, this study uncovered prognostic DNA methylation signatures associated with B-ALL relapse, present across several B-ALL subtypes. Conclusions: The findings of this study have revealed common alterations to DNA methylation across the genomes of paediatric B-ALL that establish a mechanism for clonal inheritance of gene deregulation integral to malignant phenotype. Additionally, the study establishes targets, techniques and thresholds for clinical implementation of DNA methylation loci as biomarkers for disease diagnosis, prognosis and tracking.