3q amplification is the most common genomic aberration in squamous lung cancer, suggesting that a ‘driver’ oncogene for squamous lung cancer resides within the 3q amplicon. Studying preinvasive disease has the theoretical advantage of identifying the key early molecular events in the pathogenesis of squamous lung cancer. This thesis was based on developing a method (microdissection-Molecular Copy-number Counting - μMCC) for the analysis of regional genome structure in archived biopsies and then applying this method to the analysis of the 3q amplicon in a rare collection of preinvasive bronchial lesions. Molecular Copy-number Counting was adapted and validated for the assessment of copynumber variation in degraded DNA extracted from microdissected formalin-fixed paraffin-embedded biopsies. This approach should be generally applicable, both in basic cancer research, and in the stratification of treatment based on the analysis of genome structure in clinical biopsies. A further series of experiments on high molecular weight DNA from peripheral blood raised unexpected technical issues about the effect of DNA integrity on single molecule PCR; evidence is provided suggesting that DNA sequences with very high melting temperature external to the target sequence may inhibit PCR efficiency. μMCC was applied to a series of low- and high-grade dysplastic lesions. There were a number of novel findings. Firstly, genome evolution is a dynamic process and corresponds to histological grade. All high-grade, but no low-grade lesions, showed gain or amplification of 3q relative to 3p. No low-grade lesions progressed to cancer. Secondly, the minimal commonly amplified region was narrowed to a 3.5Mb region encompassing 17 genes with the two outstanding candidates being PIK3CA and SOX2. Finally, for three individual patients, the analysis of series of biopsies sampled longitudinally allowed new observations on clonal expansion and suggested incremental regional amplification may be important in the progression of preinvasive lesions to invasive cancer.
|University College London (University of London)
|Electronic Thesis or Dissertation
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