Evolution and co-occurrence of PI3K pathway gene mutations in endometrial carcinoma molecular subtypes at the single-cell level

The PI3K pathway is altered in >85% of endometrioid endometrial carcinomas (EECs), with PTEN, PIK3CA and/or PIK3R1 mutations commonly co-occurring. Yet, the therapeutic effects of single-agent PI3K pathway inhibitors have been limited. We sought to characterize the clonal heterogeneity of EECs at single-cell resolution and define whether co-occurring PI3K pathway gene mutations affect the same or different cells. Banked frozen EECs with a high frequency of co-occurring PI3K pathway mutations (n=5 no specific molecular profile (NSMP), n=3 mismatch repair-deficient (MMRd), and n=3 POLE) were selected for single-nucleus DNA sequencing using a 317-amplicon cancer gene panel. EEC cell lines and non-malignant samples were used to define the error rate and filter false positive calls.