Fig. 3

ED and EAD induce expression of interferon-alpha genes. (A) Hierarchical supervised clustering of expression of interferon (IFN)-α genes against signatures of MDA-MB-231 cells following treatments. (B) qRT-PCR of (a) type 1 IFN genes (CXCL10, STAT1 and IRF1) and (b) interferon-responsive genes (TRIM48 and TRIM51) in MDA-MB-231 cells and (c) CXCL10 and TRIM48 in xenografts of treated mice. t test used to compare mean level of expression (± SEM) in qRT-PCR after RPL39 normalization. *Compared to entinostat or doxorubicin: *p < 0.05, **p < 0.01, ***p < 0.001. Mann–Whitney test performed, median of CXCL10 and TRIM48 expression in xenografts shown. (C) (a) Hierarchical supervised clustering of expression of IFN-α genes against The Cancer Genome Atlas (TCGA) RNA-seq breast cancer patient dataset (bars above identify different tumor subtypes (PAM50) and inflammatory cell content (immune, low–high)); (b) one-way ANOVA showed significant difference across one or more groups (#1 low, #2 medium, #3 high immune cells) and post-hoc pairwise Student t test with Bonferroni correction revealed statistically significant differences across all groups (p < 0.05); (c) IFN-α score correlation with immune infiltration. E entinostat (Ent), A all-trans retinoic acid (ATRA), D doxorubicin (Dox), Veh vehicle, Her2 human epidermal growth factor receptor 2, Lum luminal