RNA sequencing of metastatic breast patient derived organoids (PDOs) treated with control and CAF-conditioned media, in the presence and absence of Fulvestrant

To gain insight into the gene expression profile of breast patient derived organoids (PDOs) under endocrine therapy, and how cancer associated fibroblasts (CAFs) might influence gene expression and stimulate resistance, we performed RNA sequencing on three of the metastatic PDOs treated with control media and CAF-conditioned media, in the presence and absence of Fulvestrant (4-day treatment). These data revealed that Fulvestrant significantly suppressed the ER signature in the PDOs, suggesting that the ER-pathway is still active in these tumors although the patients had relapsed on ER-targeting agents (Tamoxifen, Letrozole). Overall design: Four replicates of patient #8 and #10 PDOs and 2 replicates of patient #26 PDOs grown in organoid media or CAF-CM spiked with 500 nM Fulvestrant. For PDO#8 and #10 samples were prepared in two batches.