Genetic factors are important contributors to breast cancer risk. Mutations in known breast cancer susceptibility genes (e.g BRCA1/2), account for ~25% of familial genetic risk. The remainder is likely conferred by multiple low-penetrance variants (also called SNPs). In the last five years, genome wide association studies (GWAS) have identified 170 SNPs associated with an increased breast cancer risk. Importantly, the majority of these risk SNPs lie within non-coding regions of the genome such as introns and intergenic regions, therefore regulatory elements, rather than protein-coding transcripts, are likely responsible for the associated risk. These regulatory elements are typically located more than one kilobase from their target genes and regulate transcription through long-range chromatin interactions. Our previous studies show the nearest gene to the regulatory element is not necessarily the target of the association and that there can be multiple causative genes at a risk locus. Therefore, to identify all target genes at breast cancer risk loci, we have recently used a start-of-the-art chromatin interaction technology called Capture Hi-C. This key experiment has identified more than 200 candidate breast cancer genes.
In this project, we will use multiple in vitro approaches to confirm that the newly-identified genes physically interact with the regulatory elements at breast cancer risk loci. These include eQTL analyses, chromosome conformation capture (3C)-based techniques and reporter assays. We will generate isogenic cell lines using CRISPR/Cas9 technology, which will be used to measure target gene expression, identify allele-specific chromatin interactions and assess transcription factor binding. We will also examine the function of the new genes in cancer-related pathways. Breast cells will be engineered to overexpress or silence target genes, then assayed for cell proliferation, apoptosis, response to DNA damage and breast tumour formation using an explant assays in mice. The outcomes of this project will represent a major breakthrough in breast cancer research as the products of these genes may provide new drug targets for prevention or therapy. Students will have access to unique expertise and reagents, and will acquire skills in tissue culture, CRISPR/Cas9, DNA/RNA manipulation, and other basic molecular biology techniques.
Suitable for a PhD student.