Figure 1

Hierarchical clustering of CAFs reveals interferon positive CAF subset. (A) Hierarchical clustering (HCL) of the 23 CAFs. DNA microarray data were filtered for genes that were 2-fold above or below the mean for that gene in a minimum of 3 samples. This resulted in a total of 2506 genes which are shown clustered above. (B) Magnification of the gene cluster highlighted by the red bar in Figure 1A. Further inspection of this cluster shows the upregulation of many type-one interferon genes in addition to a host of cytokines in five of the CAFs analyzed. (C) An IFN-β ELISA of DMEM (2% FBS) cultured with sub-confluent fibroblasts (3 normal breast fibroblast, 3 IFN-negative CAFs and 3 IFN-positive CAFs) for 48 hours. IFN-β ligand was only detected in the 3 IFN-positive CAF supernatents. (D) Q-RT-PCR analysis on frozen whole tumor sections corresponding to two IFN-positive and two IFN-negative CAFs. The IFN-positive CAFs (T35 and T44) showed a greatly increased level of both IFN markers IFN-β and OAS2 relative to the IFN-negative tumors (T77 and T79) (p < 0.001, by way of Bonferroni Multiple comparison test following a one-way ANOVA).