Background and strategy
High penetrance hereditary breast cancer genes account for approximately 10% of familial breast cancer (BC) cases. The largest hereditary contribution is from the combined effect of 313 low-penetrance single nucleotide polymorphisms (SNPs), measured as a polygenic risk score (PRS). The biological mechanisms through which these SNPs collectively influence BC risk remains largely unknown. However, understanding these mechanisms will inform strategies for prevention and treatment, applicable to a larger proportion of the population. We will explore the effects of PRS on BC-associated pathways in a biologically relevant cellular model using mammospheres differentiated from induced pluripotent stem cells (iPSCs), utilising a rare library of patient-derived samples from women with extreme PRS in the LifePool and Variants in Practice cohorts.
Methods
Blood samples were collected from genotyped participants and de-differentiated into iPSCs. We will acquire samples from women within the highest 1% of PRS the lowest 1%. Mammospheres were differentiated from iPSCs to generate breast-stem-like cells. RNAseq was performed on iPSCs and mammospheres to identify differences in gene expression between PRS extremes. Additionally, whole genome sequencing will be conducted on DNA extracted from extremely high or extremely low PR tumours to assess mutational signatures that may be relevant to PR.
Results
To date, 8 iPSC samples have been collected (3 high PR, 3 low PR and 2 average PR). RNAseq from iPSC samples has been analysed and a small number of genes (<20) appear to be differentially expressed between polygenic risk extremes. Mammospheres have been successfully differentiated from iPSCs, characterised by flow cytometry, and shown to express markers consistent with the mammary stem cell lineage (High CD49f and low EPCAM). RNAseq analysis of mammosphere RNA has shown a larger number of differentially expressed genes (>250) between high and low PR samples, indicating that the impact of PRS is specific to breast cells. Extreme PR tumours have been dissected and whole genome sequencing is currently in progress.
Conclusion
We are developing a mammosphere model to investigate the collective biological mechanisms of BC PRS in a breast-relevant model. Understanding these biological mechanisms may inform future clinical management strategies.