| 1. |
- Gentile, Massimiliano
(author)
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Genetic Alterations in Early Onset Breast Cancer
- 2001
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Doctoral thesis (other academic/artistic)abstract
- Cancer is in essence a genetic disease, brought about by an accumulation of alterations in genes that encode proteins responsible for the control of cell growth, cell death and the maintenance of genomic integrity. Recent years have seen the unravelling of numerous genes that are targeted in carcinogenesis. Although several genes implicated in breast cancer have been identified, a substantial proportion of breast cancer cases is not linked to any definite gene, implying that more gene targets remain to be discovered. Based on clinicopathological differences observed between early and late onset breast cancers, it has been proposed that they may be biologically different with separate genetic origins and/or development. The work included in this thesis was initiated with the intent to identify some of the genetic aberrations that characterise early onset breast cancer.The p53 protein is central in cell cycle control and alterations in its gene sequence are among the most commonly observed genetic events in human malignancies. The present study investigated the occurrence of p53 aberrations both at the protein and the gene level. Mutations were found in 17% of the cases, whereas loss of heterozygosity (LOH) and protein accumulation were observed in 42% and 46% of cases,respectively. Mutations situated in either of the L2 and L3 loops of the zinc-binding domain were found to confer a more adverse prognosis, when compared with mutations outside this region or wild-type gene (P=0.0007).LOH was further assessed for loci mapping to commonly altered chromosome regions on llq, 13q and 17p,q. High proportion of LOH was found for the BRCA1 locus and for the 11q24-q25 region where no tumour-associated gene has previously been identified. Moreover, patients with losses of this locus were observed to have a poorer prognosis (p=0.02S). In order to pinpoint the location of this putative tumour-associated gene locus, five additional microsatellite markers were scored for LOH. Association with poor prognosis, as well as with higher Nottingham Histologic Grade, narrowed the region to achromosome segment spanning approximately 500 kb. The importance of this chromosomal region was also evaluated in a group of familial breast cancers without linkage to either of the breast cancer susceptibility genes BRCA1 and BRCA2. Data demonstrated significantly lower occurrence of LOH for the majority of the markers, suggesting a less important role for the 11q24-q25 region in this subset of patients.Based on putative or known function, candidate genes located in proximity of the region identified above were selected for mutation screening. Of the investigated candidate genes, by virtue of the relatively high occurrence of alterations in its mRNA and its proposed function as mediator of apoptosis, PIG8 stood out as the most promising candidate.In addition to confirming the involvement of gene loci previously shown to be implicated in breast cancer, a region on chromosome llq was identified that may harbour a gene of importance for the disease course of early onset cases. The most promising candidate gene appears to be PIG8, which has been proposed to mediate p53-induced apoptosis.
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| 2. |
- Jiao, Xiang
(author)
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Somatic Mutations in Breast Cancer Genomes : Discovery and Validation of Breast Cancer Genes
- 2012
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Doctoral thesis (other academic/artistic)abstract
- Breast cancer is the most common cancer in women worldwide. However, the genetic alterations that lead to breast cancer are not fully understood. This thesis aims to identify novel genes of potential mechanistic, diagnostic or therapeutic interest in breast cancers by mutational analysis and whole-genome sequencing.In paper I, sequencing of 36 previously identified candidate genes in 96 breast tumors with patient-matched normal DNA determined the somatic mutation prevalence of these candidate genes and identified additional mutations in Notch, NF-κB, PI3K, and Hedgehog pathways as well as in processes mediating DNA methylation, RNA processing and calcium signaling.In paper II, comparison of massively parallel mate-pair sequencing results of a human genome before and after phi29-mediated multiple displacement amplification (MDA) revealed that MDA introduces structural alteration artifacts, with an emphasis on false positive inversions, and impairs the sensitivity to detect true inversions. Therefore, MDA has limited value in sample preparation for whole-genome sequencing for structural alteration detection.In paper III, massively parallel paired-end sequencing identified gene rearrangements in 15 hormone receptor negative breast cancers. Forty validated rearrangements were predicted to directly affect 30 genes, involved in epigenetic regulation, cell mitosis, signalling transduction and glycolytic flux. RNA interference-based assays revealed the potential roles in cell growth of some affected genes, among which DDX10 was implicated to be involved in apoptosis.In paper IV, a method for statistical evaluation of putative translocations detected by massively parallel paired-end sequencing was proposed. In an application of this method to analyse translocations detected by cancer genome deep paired-end sequencing, 76 putative translocations were classified into four categories, with the majority likely to be caused by mismapping due to repetitive regions.Taken together, this thesis provides insights into genes and pathways mutated in sporadic breast cancer genomes, which broaden our understanding of the genetic basis of breast cancer and may ultimately facilitate the diagnosis and treatment of this disease.
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| 3. |
- Kristensen, Vessela N, et al.
(author)
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Genetic variation in putative regulatory loci controlling gene expression in breast cancer
- 2006
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 103:20, s. 7735-7740
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Journal article (other academic/artistic)abstract
- Candidate single-nucleotide polymorphisms (SNPs) were analyzed for associations to an unselected whole genome pool of tumor mRNA transcripts in 50 unrelated patients with breast cancer. SNPs were selected from 203 candidate genes of the reactive oxygen species pathway. We describe a general statistical framework for the simultaneous analysis of gene expression data and SNP genotype data measured for the same cohort, which revealed significant associations between subsets of SNPs and transcripts, shedding light on the underlying biology. We identified SNPs in EGF, IL1A, MAPK8, XPC, SOD2, and ALOX12 that are associated with the expression patterns of a significant number of transcripts, indicating the presence of regulatory SNPs in these genes. SNPs were found to act in trans in a total of 115 genes. SNPs in 43 of these 115 genes were found to act both in cis and in trans. Finally, subsets of SNPs that share significantly many common associations with a set of transcripts (biclusters) were identified. The subsets of transcripts that are significantly associated with the same set of SNPs or to a single SNP were shown to be functionally coherent in Gene Ontology and pathway analyses and coexpressed in other independent data sets, suggesting that many of the observed associations are within the same functional pathways. To our knowledge, this article is the first study to correlate SNP genotype data in the germ line with somatic gene expression data in breast tumors. It provides the statistical framework for further genotype expression correlation studies in cancer data sets.
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