Figure 3. SMYD2 knockdown abrogates alpelisib-induced changes in gene expression, including ER-dependent transcription.

(A) Heatmap of RNA-seq data showing the subset of genes in MCF7 cells regulated by alpelisib treatment (3,995), with and without SMYD2 knockdown (1,248 differential, log₂ fold change >0.5 and adjusted p value <0.1). Cells were treated with 1 μM alpelisib for 24 h before collection (n = 3 technical replicates).

(B) Plot of C2 pathways from gene set enrichment analysis (GSEA) in SMYD2 knockdown compared to control in DMSO and alpelisib treatment conditions. All gene sets shown were significant with a p value of <0.05. Nominal p values and false discovery rate (FDR) adjusted p values were calculated using the GSEA package. Normalized enrichment score (NES) for each gene set is indicated on the x axis.

(C) GSEA plot of the Dutertre estrogen response gene set in SMYD2 knockdown compared to control in both DMSO and alpelisib treatment conditions. Nominal p values and FDR adjusted p values were calculated using the GSEA package.

(D) Gene set variation analysis (GSVA) results of estrogen-responsive gene sets in ER+ patient samples from the TCGA and METABRIC datasets corresponding with median SMYD2 mRNA level. Data are shown as median with interquartile range and analyzed using a two-tailed Student’s t test.