Isoform-Specific Gene Regulation by Progesterone Receptors Drives Divergent Phenotypes in Breast Cancer Cells [RNA-Seq]

Exposure to progesterone is a recognized risk factor for breast cancer, and PGR polymorphisms are associated with various malignancies. The two progesterone receptor (PR) isoforms, full length PR-B and truncated PR-A, are expressed from the PGR gene in breast tissue and play crucial roles in normal physiology and breast cancer progression. An imbalance in the expression ratio of these isoforms, favoring increased levels of PR-A, is common in breast cancer and is associated with resistance to tamoxifen in Luminal A-type tumors. Notably, PRs have recently been implicated in promoting endocrine resistance and driving the expansion of cancer stem-like cell (CSC) populations. Despite this insight, the isoform-specific molecular and epigenetic mechanisms underlying PR action in ER+ breast cancers remain understudied. Phenotypic studies of T47D cell lines that express exclusively PR-A or PR-B showed that PR isoforms regulate divergent cell fates. PR-B expressing cells have a higher proliferation rate, while PR-A expressing cells produce more mammospheres. We profiled progesterone-driven gene expression in cells grown in both adherent (2D) and mammosphere (3D) growth conditions and found differential gene regulation by PR-A and PR-B that is consistent with the observed divergent phenotypes. We then performed CUT&RUN to identify the genomic binding patterns unique to each PR isoform and their suite of target genes. Our findings indicate that PR-A acts as a regulator of the cell cycle and senescence, while PR-B plays a pivotal role in metabolism and intracellular signaling. Our genomic profiling of PRs in this model system has unveiled novel isoform-specific functions of PR. This work has shifted our prior understanding of the role of PRs in gene regulation, offering potential insights for therapeutic interventions in ER+ breast cancer.