Prostate cancer is a clinically heterogeneous disease, with manifestations ranging from a rapid and often fatal progression, to indolent disease. Unfortunately, current clinicopathological criteria cannot differentiate men whose tumours require immediate and aggressive therapy from those in which active surveillance may be more appropriate. Both PTEN deletion and ETS gene fusions are biomarkers with potential to aid in prostate cancer clinical management. In this thesis, I postulate that PTEN and fusion gene rearrangements may be associated with specific genomic changes, and might also have general impact on the genomic landscape of prostate cancer. A meta-analysis of somatic copy number alterations (CNAs) examined 662 unique prostate cancer patient samples consisting of 546 primary and 116 advanced tumours derived from eleven publications. Normalization, segmentation and identification of corresponding CNAs for meta-analysis were achieved using established commercial software. The CNA distribution in primary disease was characterized by losses at 2q, 3p, 5q, 6q, 8p, 12p, 13q, 16q, 17p, 18q and 10q (PTEN), and acquisition of 21q deletions associated with the TMPRSS2:ERG fusion rearrangement. Unsupervised analysis identified five genomic subgroups. Parallel analysis of advanced and primary tumours indicated that PTEN genomic deletions and the gene fusion were enriched in advanced disease. A supervised analysis of PTEN deletions and gene fusions demonstrated that PTEN deletion was sufficient to impose higher levels of CNA. Moreover, the overall percentage of the genome altered was significantly higher when PTEN was deleted, suggesting that this important genomic subgroup was likely characterized by intrinsic chromosomal instability. Candidate genes in each of the recurrent CNA regions characteristic of each subgroup showed that signalling networks associated with cancer progression and genome stability were likely to be perturbed at the highest level in the PTEN deleted genomic subgroup. Therefore classification of primary prostate cancer according to PTEN deletions, but not the gene fusion, was associated with greatly increased levels of CNA. Collectively, the impact of PTEN loss resulted in a significantly greater frequency and extent of alteration, and heightened genomic instability with concomitant pathway disruptions. / Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2014-04-29 14:20:06.02

Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

Phytophthora root and stem rot is the most destructive soybean soil-borne disease worldwide and can be managed using soybean cultivars with genes conferring resistance to <i>Phytophthora sojae</i>. Here we show that soybean <i>Rps11</i> is an ~27-kb nucleotide-binding site leucine-rich repeat (NLR) gene that confers broad-spectrum resistance to the pathogen. This giant gene is located in a genomic region containing 12 unusually large NLR genes of a single origin and was formed by rounds of intergenic/intragenic unequal recombination that involves the promoter regions and the LRR regions. Comparison of the genomic region in the Rps11 donor line with its corresponding regions in 29 diverse soybean genomes revealed drastic regional diversification including NLR copy number variation ranging from 5 to 23, and absence of allelic copy of <i>Rps11</i> in all 29 genomes. This study highlights innovative evolution and complexity of an NLR cluster and enables precise selection of <i>Rps11</i> for cultivar improvement.