The utilisation of microfluidic qPCR technology for the identification of novel cancer biomarkers

Cancer is a major cause of death worldwide causing 1 in 6 deaths globally with approximately 14 million new cases and 8.8 million cancer related deaths in 2015. This figure is expected to increase to 21.7 million cases and 13 million deaths by 2030. In Ireland, an average of 30,000 new cases of cancer are diagnosed each year. The number is also expected to rise to over 40,000 per year by 2020. A key focus to reverse this trend is the identification of new prognostic markers and therapeutic targets that can be used to predict the incidence or outcome of the disease. These targets can also be used to screen populations to identify symptomatic patients, identify differential diagnosis and for the clinical staging of cancer. The quest for a better understanding of the carcinogenesis process has led to impressive growth in the field of large-scale and high-throughput biology which has become a driving force behind the emergence of new technologies. Large scale gene expression profiling is an essential tool for many biological and medical investigations. Higher throughputs and increased levels of specificity coupled with reduced volumes of samples and reagents is a dominant factor. . The development and application of a microfluidic platform to analyse biological samples at a rate of approximately one thousand data points per hour is demonstrated in this thesis. Utilisation of such a platform gives an advantage over many traditional systems and allows for the manipulation of smaller quantities to achieve corresponding biological outcomes. This thesis investigates the application of microfluidic gene expression profiling to identify biomarkers in colorectal and breast carcinoma, envisioning that future validation tests using a microfluidic platform could produce an expression assay to aid the stratification of the disease. The focus is on candidate genetic targets that are regulating extracellular matrices production which are central components of a tumour’s microenvironment, possessing key roles for tumour formation, growth and potential metastatic spread. In two genetic studies of colorectal and breast cancer malignancies, a number of genes from the extracellular matrix family emerge as being statistically differentially expressed. Correlations of the genes with the histopathological parameters along with heterogeneity of the tumours are investigated also. Genetic targets identified could potentially serve as molecular markers in screening, diagnosis and treatment strategies for the individualised care of patients in the future.