Mutations in the PIK3CA gene are the most frequent genomic alterations in estrogen receptor (ER)-positive breast cancers. Direct pharmacological inhibition of PI3K signaling is therefore an attractive clinical strategy and a number of PI3K pathway inhibitors are currently under clinical development. Unfortunately, although the majority of ER-positive PIK3CA-mutant patients respond, mechanisms of resistance to these inhibitors inevitably emerge. By studying both mouse models and human samples, our laboratory has previously uncovered that inhibition of PI3K pathway increases ER transcriptional activity, which in turn renders cells more susceptible to endocrine therapy. The mechanisms by which ER and PI3K signaling pathway regulate each other in breast cancer cells, however, remain elusive.

To better understand the cross-talk between the PI3K pathway and the ER transcriptional program, we developed an unbiased transposon activation mutagenesis screen with the goal of identifying modulators of resistance to PI3K inhibitors in ER-positive tumors. Among the genes identified, we found a number of key regulators of ER function including the pioneer transcription factors FOXA1 and PBX1. We further confirmed that FOXA1 and PBX1 expression and transcriptional activity was enhanced upon PI3K inhibition and validated these observations in both xenograft models and samples from patients undergoing treatment with the PI3Ká inhibitor BYL719. Moreover, chromatin imunoprecipitation (ChIP)-sequencing against ER and FOXA1 demonstrated that these factors occupy the same genomic regions, and their binding is increased upon PI3K inhibition. Silencing FOXA1 or PBX1 impaired the activation of the ER-dependent transcriptional program following PI3K blockade and sensitized cells to PI3K inhibition.

To better understand the role of FOXA1 and PBX1 in the ER-PI3K crosstalk, we have then studied in detail the chromatin changes upon BYL719 treatment using transposase-accessible chromatin using high-throughput sequencing (ATAC-seq) in breast cancer cells. Epigenomic profiling using ATAC-seq is also being done on patient samples collected before BYL719 administration (pre-treatment) and during therapy (on-treatment). ATAC-seq and RNA-seq data from the same patients will be integrated using novel computational approaches.

These analyses will help to dissect the ER-dependent epigenetic changes occurring upon PI3K inhibition and how the cells use these chromatin modifications to adapt to the pharmacological stress. Elucidating the interconnection between the PI3K pathway and ER activity may uncover novel mechanisms of resistance to either PI3K inhibitors or endocrine therapy in ER-positive breast cancer patients.

Citation Format: Eneda Toska, Hatice Osmanbeyoglu, Moshe Elkabets, Carmen Chan, Pau Castel, Maura Dickler, Scott Armstrong, Christina Leslie, Maurizio Scaltriti, Baselga José. Epigenetic regulation of estrogen receptor transcription by the PI3K pathway in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 885.