Ponnampalam, SN;
(2016)
A blood-based gene expression and signalling pathway analysis to differentiate between high and low grade gliomas.
Doctoral thesis , UCL (University College London).
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Abstract
Introduction: Brain tumours are the 17th most common cancer worldwide. Gliomas are the most common of the primary brain tumours and are highly malignant. / Objectives: (a) To undertake gene expression profiling of the blood of glioma patients to determine key genetic components of signalling pathways (b) To develop a panel of genes that could be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-glioma and control samples. / Methods: Blood samples were obtained from glioma patients, non-glioma and control subjects. Ten samples each were obtained from patients with high and low grade tumours respectively, ten samples from non-glioma patients and twenty samples from control subjects. Total RNA was isolated from each sample after which first and second strand synthesis was performed. The resulting cRNA was then hybridized with the Agilent Whole Human Genome (4x44K) microarray chip according to the manufacturer's instructions. Universal Human Reference RNA and samples were labeled with Cy3 CTP and Cy5 CTP respectively. Microarray data were analyzed by Agilent Gene Spring 12.1V software using stringent criteria which included at least a 2-fold difference in gene expression between samples. Statistical analysis was performed using the unpaired student T-test with a p-value < 0.01. Pathway enrichment was also performed with key genes within these pathways selected for validation with ddPCR. / Results: The gene expression profiling indicated that were a substantial number of genes that were differentially expressed with more than a 2-fold change (FDR corrected value < 0.01) between each of the four different conditions. We selected key genes within significant pathways that were analyzed through pathway enrichment. These key genes included regulators of cell proliferation, transcription factors, cytokines and tumour suppressor genes. / Conclusion: In this study, we have shown that key genes involved in significant and well established pathways, could possibly be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-gliomas and control samples.
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