Fig. 3: Loss of NELF-E suppresses EMT in a SOX9-SLUG overexpression MCF7 cell line model.

a Barplot showing the top perturbed pathways from Molecular Signatures Database (MSigDB) in Doxycycline (Dox)-treated MCF7ras+SS cells compared to the vehicle control. b Volcano plot depicting the significantly upregulated genes (n = 1750) and downregulated genes (n = 2223). Select mesenchymal/stemness-related genes are labeled in red, while epithelial genes are labeled in blue. adj. p-value ≤ 0.05; |fold change| ≥ 1.5. p-value was calculated using DESeq2 package (see details in “Methods”) c Western blot analysis for different markers in Dox-induced MCF7ras+SS cells transduced with scrambled or two independent shRNAs targeting NELF-E. GAPDH was used as the loading control. d GSEA plot of shNELF-E+Dox vs SCR+Dox cells. p-value was calculated from gene set enrichment analysis. (see detail in “Methods”). e Representative images and quantification of the migration and invasion assays. MCF7ras+SS cells were transduced with scrambled or NELF-E shRNA and treated with Dox to induce SOX9 and SLUG expression for 72 h prior to the assays (n = 3). Scale Bar = 100 μm. f Representative images and quantification of the sphere-formation assay. MCF7ras+SS cells were transduced with scrambled or NELF-E shRNA, followed by 72-h Dox treatment. Cells were seeded at a density of 10K per well, and the number of spheres was counted 5–7 days later (n = 4). Scale Bar = 100 μm. g Representative images and quantification of the soft agar assays for SCR+Dox and shNELF-E+Dox cells (n = 3). h Flow cytometry analysis and quantification of the CD24^low/CD44^high population in NELF-E KD+Dox cells compared to SCR+Dox cells (n = 3). Blots and images are representative of at least three independent experiments. p-values in (e–h) are determined by a two-tailed Student’s t-test. Mean ± SD is represented by bar graphs. Source data are provided as a Source Data file.