Background and strategy
High penetrance hereditary breast cancer (HBC) genes only account for around 10% of all familial breast cancer (BC) cases. The largest hereditary contribution is from >300 common low penetrance single nucleotide polymorphisms (SNPs) whose combined effect, measured as a polygenic risk score (PRS), can be substantial. How the genes that are the target of these SNPs collectively influence BC risk remains largely unknown. Understanding the biological mechanism through which this occurs will provide insights into novel strategies for prevention and treatment that would be applicable to a large proportion of the population. We aim to explore the effects of PRS on BC associated pathways in a biologically relevant cellular model by creating mammospheres from induced pluripotent stem cells (iPSCs), using a rare library of patient-derived materials from women in the highest and lowest 1 percentile of PRS.
Methods
184 women with a PRS above the 99th centile of the Australian population (the highest at 99.997th centile) and 50 women below the 1st centile were identified from genotyped individuals in the LifePool and Variants in Practice studies. Fresh blood samples are requested from participants and iPSCs are generated by the iPSC Derivation and Gene Editing Facility at the Murdoch Children’s Research Institute.
RNAseq will be performed on iPSCs and mammospheres to identify differences in gene expression between PRS extremes. Whole genome sequencing of long-term cultured cells will be used to assess mutational signatures arising in different PRS contexts, either alone or in iPSCs edited by CRISPR to carry a mutation in a high or moderate risk HBC gene. Whole genome sequencing and RNAseq will be carried out on tumour samples from patients with extremely high or low PRS.
Results
RNA has been extracted from iPSCs and analysed for differential expression. Mammospheres have been successfully created from iPSCs.