Extended Data Fig. 10: Cytokine and chemokine analysis of tumor cell lines.

(a)Table containing a curated list of cytokines and chemokines directly relevant to monocyte/macrophage polarization, activation and impact on T cell (b) Expression of monocyte and macrophage- related chemokine and cytokine genes in ER+ IDC (n = 532) and ILC (n = 180) patient samples from The Cancer Genome Atlas (TCGA) cohort. Table lists log 2 TPM normalized counts with standard deviation. (c) Expression of monocyte and macrophage- related chemokine and cytokine genes in ER+ IDC (n = 1098) and ILC (n = 122) patient samples from Metabric cohort. Table lists log 2 TPM quantile normalized counts with standard deviation. (d) Expression of monocyte and macrophage- related chemokine and cytokine genes in ER+ IDC (n = 532) and ILC (n = 180) patient samples from SCAN-B cohort. Table lists log 2 FPKM normalized counts with standard deviation. For (b),(c) and (d) highlighted in yellow are the concordant genes found to have a consistent pattern across TCGA, Metabric and SCAN-B cohorts (e) Analysis of cytokine and chemokine concentrations (pg/ ml) using MSD platform in conditioned media collected from ER+ IDC cell lines (n = 4: T47D, MCF7, BT474, ZR75-1) and ER+ ILC cell lines (n = 4: SUM44, MM134, MM330, BCK4) used in macrophage polarization experiments shown in Fig. 7c,d. Values in red denote group medians for each analyte. Non-parametric Mann-Whitney two-sided T test was used for statistical analysis (f) Histograms showing comparison of median fluorescence intensity (MFI) for HLA-DR expression in monocytes subjected to control (M1 or M2) polarizing conditions or test with IL-15 or IL-33 across 3 healthy donor samples. (g) Histograms showing comparison of median fluorescence intensity (MFI) for CD206 expression in monocytes subjected to control (M1 or M2) polarizing conditions or test with IL-15 or IL-33 across 3 healthy donor samples.