Microarray gene expression data from MCF-7 and MPiFR cells

The PI3K inhibitor (PI3Ki) alpelisib in combination with fulvestrant is currently FDA approved for the treatment of advanced ER+ breast cancer following progression on endocrine therapy. It is unclear which treatment strategy is beneficial following progression on the combination of PI3Ki and fulvestrant, and therefore, identification of novel therapeutic targets is needed. We used microarrays to detail the global programme of gene expression in cells resistant to the combination of PI3Ki and fulvestrant (MPiFR). The parental sensitive cell line, MCF-7, was used for comparison. The gene expression analysis revealed a significant number of genes altered in the MPiFR cells vs. MCF-7 cells. We found a significant upregulation of cell cycle-related genes, particularly CDK6, CDK2, and cyclin E1 and E2 in MPiFR vs. MCF-7 cells. The combined PI3Ki, alpelisib, and fulvestrant- resistant cell line is derived from MCF-7 and was established through long-term treatment with fulvestrant and increasing concentrations of PI3Ki. Total RNA from MCF-7 and MPiFR cells was extracted and arrayed separately in Human Transcriptome Array 2.0 (HTA, Affymetrix).