Fig. 4

NRAS overexpression induces basal-like features in a human luminal DCIS model SUM225. A SUM225 cells overexpressing N-Ras and the counterparts carrying the vector control were cultured for 5 weeks. The RNA-seq data generated from these SUM225 cells and from the same CPTAC breast cancer cohort as in Fig. 3B were combined, and then, the top 1000 most variable genes across combined samples were used to perform unsupervised hierarchal clustering. B Gene Set Enrichment Analysis on Hallmark gene sets was performed using signed –log10 p values from limma results. Gene sets represented as red bars are up-regulated, while blue bars are down-regulated in NRAS-overexpressing SUM225 cells. C SUM225 cells carrying a DOX-inducible vector to overexpress NRAS were seeded with or without DOX in low attachment dishes for mammosphere formation. Normal spheres that are mostly round with a smooth boundary were counted as normal (top). The disorganized spheres usually have irregular shapes with cell masses that protrude from the boundary. Bar = 200 µm. Whether the portions of disorganized spheres are more common in NRAS overexpressing cells (+ DOX) in two separate experiments was examined by Fisher’s exact test (bottom)