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UBC Theses and Dissertations

Identification of novel genetic alterations in the progression of lung and oral cancer Garnis, Cathie


The major etiological factor for oral and lung cancer is tobacco and both diseases have poor survival and high recurrence rates. In order to facilitate early diagnosis and lay the groundwork for new treatment strategies, we must determine the genetic alterations that drive these diseases. Due to the genomic instability associated with late stage tumors, early causal genetic changes will be best identified by studying both premalignant lesions and invasive tumors. The overall objective of this thesis is to identify genetic alterations that are associated with the progression of lung and oral cancer and to further assess if these changes are of biological importance. This will help to identify candidate genes for use as diagnostic markers and/or therapeutic targets. The first genome-scanning technique used was a PCR-based technique: RAPD-PCR. From this analysis we cloned and localized 15 recurrent alterations in the lung and oral samples. Two of these alterations, 13ql4 and 8q22, were further fine mapped using microsatellite analysis to reveal two candidate genes: AKAP220 and ST7. The remaining regions identified with RAPD-PCR were then fine-mapped by comparative genomic hybridization (CGH) using a bacterial artificial chromosome (BAC) array. We called this array the regional array as it contained 26 selected regions as well as complete coverage of chromosome arms lp, 3p, and 5p. This methodology identified numerous novel regions of alteration and highlighted the value of the premalignant lesion: we found that there were fewer alterations in the premalignant lesions as well as some discrete changes that were masked in the later stage samples. We expanded this approach by using a new CGH array that covers the entire genome and have profiled various histopathological stages in both oral and lung cancer. This new tool is ideal for novel gene discovery as no prior knowledge of regions is required. Whole genome profiling of different histopathological stages for both oral and lung cancer has given us insight into the genetic alterations associated with the progression of these diseases. While oral and lung cancer share some similarities, such as the early loss of chromosome 3p and 9p, there are also some drastic differences. By combining high resolution CGH tiling arrays with precious pre-invasive material we have for the first time produced a comprehensive view of oral and lung pre-invasive lesion genomes. In doing this, we have identified numerous recurrent novel genetic alterations and have shown the biological relevance of these alterations through expression analysis. In the future these candidates will serve as potential diagnostic makers and therapeutic targets.

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