Fig. 7: Chemokine expression in A3250 and in human IBC.
a mRNA-Seq analysis of human chemokines in A3250 tumors in vivo and cells in vitro, shown as log2(FPKM). b qPCR for chemokines as indicated in A3250, SUM149 and MDA-MB-231 cells in vitro. n = 3 biologically independent samples. Data are presented as mean values ± SD. Two independent experiments were performed. c qPCR for CCL2 expression in A3250 cells in vitro compared to the SUM149 and eight non-IBC cell lines. n = 3 biologically independent samples. Data are presented as mean values ± SD. Two independent experiments were performed. RU = relative units. d Chemokines in supernatants of cells as indicated, detected with Olink proteomics. Select chemokines are shown, that were expressed by mRNA and present in Olink Inflammation panel. Heatmap indicates matrix values, data scaled by row. e Boxplot showing the distribution of FPKM values for CCL2, CXCL5, and CCL20 chemokines in 1222 TCGA breast cancer samples. Each point represents an individual sample. Dotted line indicates average FPKM for the A3250 tumor (n = 3). CCL2 expression in IBCs and non-IBCs by analysis of human microarray datasets E-MTAB-100624 (f) and GSE2259726 (g), measured as the percentile rank of signal intensity for the maximally expressed probe for CCL2. Box extends to 25th and 75th percentiles, whiskers to the 10–90 percentile and black line denotes the median. The significance of the difference in distributions of percentile ranks in IBC vs non-IBC samples was assessed using Wilcoxon rank sum test. h–j Expression of CCR2 on myeloid cell subsets in A3250 tumors, blood and lungs, determined by flow cytometry. Fraction of CCR2+ CD11b+ cells. n = 4 biologically independent samples (h); fraction of CCR2+ Ly6Chi or CCR2+ Ly6Clo cells (i); representative FACS plots of CD11b+ CCR2+ cells in blood, tumors and lungs (j). A Type III Analysis of Variance with Satterthwaite’s method determined a significant difference between the three groups (p = 4 × 10−5), followed by a Linear Mixed Model fit by REML and t test using Satterthwaite’s method with Bonferroni correction (blood, tumor p = 1.7 ×10−5; lung, tumor p = 6.7 × 10−5). Black line on the plot indicates mean ± SEM (h) ***p < 0.001. FPKM = Fragments Per Kilobase of exon per Million mapped reads. Source data are provided as a Source Data file.
