Transcriptomically-inferred PI3K activity and stemness show a counterintuitive correlation withPIK3CAgenotype in breast cancer

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>The development of reliable, prognostically informative molecular tests to direct targeted cancer therapy is a major challenge. In 2019, the PI3Kα inhibitor alpelisib was approved for the treatment of advanced breast cancer, in combination with the oestrogen receptor degrader fulvestrant, with some evidence for improved therapeutic response in patients classified as having tumours which were positive for mutation in <jats:italic>PIK3CA</jats:italic>, the gene encoding PI3Kα. Using human pluripotent stem cells, we recently demonstrated that the <jats:italic>PIK3CA</jats:italic><jats:sup><jats:italic>H1047R</jats:italic></jats:sup> oncogenic hotspot variant shows marked <jats:italic>PIK3CA</jats:italic> allele dose-dependent activation of PI3K signalling and induction of self-sustained stemness. Together with recent discoveries of multi-copy and double-<jats:italic>cis PIK3CA</jats:italic> mutations in human cancers, this calls for a re-evaluation of the <jats:italic>PIK3CA</jats:italic> genotype-phenotype relationship and the current use of binary stratification by <jats:italic>PIK3CA</jats:italic> mutation status. Using computational analyses, we thus investigated the relationship between <jats:italic>PIK3CA</jats:italic> mutational status, PI3K activity/signalling strength and stemness. Stemness and PI3K activity scores were calculated using open-source methods and well-established transcriptional signatures. We report that a high PI3K pathway activity score, but not the presence of <jats:italic>PIK3CA</jats:italic> mutation <jats:italic>per se</jats:italic>, predicts increased breast cancer dedifferentiation and higher stemness, correlating with reduced overall survival. Our data (1) corroborate reports that the presence of a <jats:italic>PIK3CA</jats:italic> mutation per se does not predict high PI3K pathway activation or poor prognosis; (2) suggest that stratification of breast cancer for PI3K-based therapy might benefit from the use of a PI3K pathway activity score rather than binary <jats:italic>PIK3CA</jats:italic> mutation status alone; (3) suggest that combination of PI3K pathway inhibitors with differentiation-promoting treatments warrants evaluation in aggressive breast cancers with high PI3K activity and stemness scores.</jats:p>

NODAL/TGFβ signalling mediates the self-sustained stemness induced by PIK3CAH1047R homozygosity in pluripotent stem cells

“…BYL719 (alpelisib; Novartis), the PI3Kα-selective inhibitor used in our cellular studies, was recently approved for use in combination with anti-oestrogen therapy in oestrogen receptor-positive breast cancers ( André et al, 2019 ). In a separate study focusing on human breast cancer, we have described the use of computational analyses to demonstrate a strong positive relationship between a transcriptomically derived PI3K activity score, stemness gene expression and tumour grade in breast cancer ( Madsen et al, 2020 preprint). Previous reports have suggested a role for NODAL in driving breast cancer stemness and aggressive disease ( Bar-Eli, 2012 ; Margaryan et al, 2019 ), with potential links to mTORC1 activation ( Katsuno et al, 2019 ; Jewer et al, 2020 ).…”