cRNA preparation, purification and labelling, array hybridisation and scanning were performed Saracatinib in vitro according to the manufacturer’s protocol (Illumina). Gene expression was compared between (I) tumour spheroids, (II) tumour cells only sorted out from co-cultures

and (III) co-culture spheroids. Four biological replicates (monocytes from different donors) for co-culture spheroids and two replicates for tumour spheroids were studied using Illumina HumanRef-8 v.2.0 chips. Illumina BeadStudio was used for background correction and generating average signal intensity. R/Bioconductor 30 was used for quantile normalisation 31. Probes showing low variability were discarded by applying interquartile filter (IQR=0.25). A linear model 32 was employed by controlling the number of false positives by false discovery rate (FDR) with adjusted p-value of ≤0.05 33. A log2 fold change signal threshold (log2(FC)≥1.0) was applied for comparison of (I) and (II), and (log2(FC)≥1.5) for comparison of (II) and (III). MultiExperiment Viewer 34, 35 was used for hierarchical clustering, setting a Euclidean Nutlin-3a cell line distance as the measure of dissimilarity and average linkage as the linkage method. To identify biologically relevant regulatory processes and pathways, MetaCore with a FDR adjusted p-value of ≤0.05 was used. Primers were designed using Primer-3 (Supporting Information Table 3). Real-time

PCR was performed with Stratagene Mx3000P (Agilent). All gene expressions were normalised to Selleckchem Pembrolizumab housekeeping gene hypoxanthine phosphoribosyltransferase (HPRT). Tumour cells were labelled with anti-EpCAM-FITC, stained with propidium iodide (15 μg/mL; Sigma) and analysed by flow cytometry. Pre-cleared cell culture supernatants

(days 5–8) were used for cytokine measurement (Bio-Plex Pro Human Cytokine Groups I and II, BioRad). Culture medium with 5% HS was used as blank and diluent. Detection was carried out with Luminex 200TM. Results were acquired using IS 2.3 software. CCL8 and CCL13 were detected using Duoset ELISA Development Systems (R&D Systems). Samples were diluted and prepared according to manufacturer’s protocol. Culture medium with 5% HS was used as the blank. Supernatants were incubated at 37°C, 5% CO2, 30 min to allow pH equilibration before assay. Total white blood cells (WBC) were obtained from buffy coats after red blood cell lysis. Totally, 7.5×105 WBC were seeded onto cell culture inserts (BD) with 8.0 μm pore sizes, incubated with supernatants in wells for 1 h. T cells (CD3, CD4, CD8) that trans-migrated through the inserts were distinguished by fluorescence labelling and analysed by flow cytometry (LSRII, BD). Countbright beads (Invitrogen) were used for cell number quantification. WBC from six donors and supernatants from three replicates (spheroid cultures) were used. Tumour cells from co-culture spheroids were labelled with anti-EpCAM-FITC followed by anti-FITC microbeads (Miltenyi) for magnetic sorting into tumour cells and TAMs.