Extended Data Fig. 4: ARID1A loss mediates a basal-like gene expression.
(a) Volcano plot; x-axis is log2 fold change and y-axis represents -log10(P); n=18 samples, statistical by DESeq2. (b) mRNA levels of luminal and basal-like/stemness markers in control and ARID1A KO cells. Error bars=mean ±SEM, n=2 biologically independent samples, center values are means. *P value<0.05, ** P value<0.01, Student’s two-sided t test. (c) Cropped western blot of indicated antibodies. (d) mRNA levels of aforementioned markers in MCF7 upon addition of doxycycline (DOX) knockdown of ARID1A. Error bars=mean ±SEM, n=2 biologically independent samples, center values are means. *P value<0.05, ** P value<0.01, Student’s two-sided t test. Also shown are ARID1A and vinculin levels. (e and f) Cropped western blot with indicated antibodies in BT474 or MDA-MB-361 cells expressing sgNT and two sgRNAs against ARID1A. (g and h) Enrichment of basal-like signatures in BT474 (Charafe breast cancer luminal vs. basal down) or MDA-MB-361 (Huper breast basal vs. luminal up) upon ARID1A KO. (n=6 per cell type, nominal P values and FDR adjusted P values were calculated using GSEA package.) (i and j) Enrichment of basal-like and estrogen response signatures in MCF7 after SMARCB1 or SMARCE1 knockout; n=8 per gene knockout, nominal P values and FDR adjusted P values were calculated using GSEA package. (k) Enrichment of basal-like signatures in ARID1A wild type vs. biallelic loss of ARID1A of patient sample pairs (*, FDR < 0.25;). n=2 for each patient pair, nominal P values and FDR adjusted P values were calculated using GSEA package).
