CNVs and familial breast and ovarian cancer
BRCA1 pathogenic variant carriers experience a high risk of developing breast and ovarian cancer, however, differences in risk vary greatly between individuals. The advent of genetic testing has presented an increasing need to better understand these differences to enable reliable risk prediction. However, much is still unknown about genetic factors associated with cancer risk, including the biological mechanisms that underlie their effects. Copy number variants (CNVs) are a form of genetic variation that play a significant role in many complex diseases and has been implicated in numerous familial cancer syndromes. The potential for CNVs to modify the level of risk in BRCA1 pathogenic variant carriers has only recently been explored in a genome wide association study conducted by the international CIMBA consortium, which identified 2 gene loci that were associated with breast or ovarian cancer risk. The aims of this project were (1) to develop a methodology for prioritising modifier CNVs for functional analyses, and (2) carry out functional analysis to determine the impact of CNVs. I hypothesise that (1) a copy number deletion of a candidate modifier results in a decreased expression of that gene, which in turn confers the associated risk reported by Walker et al., and (2) that a CNV deletion of BRCA1 would have a greater functional impact due to effects on BRCA1 expression. Twelve candidate modifier genes were prioritised based on their relationship between copy number status and mRNA expression in either breast or ovarian tumour tissue. The CIMBA study highlighted CY2A7 for its strong association with ovarian cancer, although a relationship between copy number and expression was only found in breast tumour data. Interestingly, the expression of the nearby enhancer of EGLN2 was strongly correlated with CYP2A7 copy number. DEAF1 was prioritised for functional studies as it showed a strong positive correlation between copy number and expression level, as well as a potential indirect interaction with BRCA1 via LMO4. BRCA1 was also chosen, as an ongoing CIMBA study showed that CNVs overlapping BRCA1 resulted in higher risks of breast cancer, compared to SNP pathogenic variants. Transient siRNA knockdown experiments were carried out in the following cell lines; SKOV-3 for DEAF1, and MCF10A for BRCA1. Cell seeding density, different transfection methods and media conditions were tested and optimised to help achieve optimal knockdown efficiency for both cell lines. This study has established a process of prioritisation and selection of candidate genes for functional analysis and laid a methodological foundation for the in vitro functional analyses of candidate modifiers.
Advisor: Walker, Logan; Lattimore, Vanessa
Degree Name: Bachelor of Biomedical Sciences with Honours
Degree Discipline: Department of Pathology and Biomedical Sciences
Publisher: University of Otago
Keywords: BRCA1; breast cancer; ovarian cancer; CNVs; risk; copy number variants
Research Type: Thesis