RNA-seq to profile the transcriptome changes induced by the EZH2 degrader MS1943

To gain mechanistic insights into how MS1943 induces cell death, MDA-MB-468 cells were treated with 5 µM of MS1943 or DMSO control and changes of gene expression were assessed after 3 days of treatment. Interestingly, MS1943-treated cells were characterized by a unique set of deregulated genes that could readily separate them from control cells. We identified 8,730 significant differentially expressed genes with a false discovery rate (FDR) at 5%, in which 2,120 genes have an absolute log fold change above 1. We next performed gene set enrichment analyses (GSEA) that capture pathways perturbed towards both directions simultaneously using the 24,448 ranked genes identified in our dataset and annotated in ENSEMBL (version 94) against the KEGG pathways and the hallmarks gene set collection (MSigDB V6.2). Induction of the unfolded protein response (UPR) / endoplasmic reticulum (ER)-stress pathway was commonly identified using both types of analyses and we therefore decided to pursue this further. Overall design: Examination of difference in gene expression in one breast cancer cell line, MDA-MB-468, between treated with 5 µM of MS1943 (n=2) and treated with DMSO as control (n=2).