(D) CSF1 protein level was analyzed from castrated mice (day 2 and day 35 castration). by: 1) the moving offset (|equals 2 for migration, and 1 for proliferation.(TIF) pcbi.1007344.s016.TIF (102K) GUID:?333257A7-0165-44EE-96B5-E57479A66E0E S16 Fig: The strategy for generating sprouts during model initialization. If 0= 0; otherwise, follows a normal distribution (14 1.3 (fold change of presence TAM to absence TAM), we totally obtained 11 over-expressed ligand genes (e.g., TNFSF10, VEGFA) and 6 receptor genes from the co-cultured LNCAP cells; and 13 ligand genes (TNFSF10, SPP1, etc.) and 12 receptor genes (e.g., EGFR) in the co-cultured 22RV1 cells. At the presence of TAMs, we found that 1) LNCaP positively expressed AR signaling axis; 2) 22RV1 secreted CSF1 and TNFSF10 (TRAIL), which potentially induced TAM recruitment and polarization, and Treg proliferation. Similarly, we obtained 27 overexpressed ligand genes (e.g., IL10) and 30 receptor genes (e.g., CSF1R) from M2 IACS-9571 macrophages co-cultured with LNCAP cells, compared with the M2 cells without co-culture. Also, 31 ligand genes (IL10, TNFSF10, and VEGFA, etc.) and 46 receptor genes (CSF1R, TGFBR1, etc.) were over-expressed in M2 macrophage co-cultured with 22RV1 cells. Fig 2A shows the top-ranked overexpressed ligand and receptor genes in these three types of cells (S1 Data). As described in the above section, we determined the potential directional connections with high confidence scores (from iRefWeb) and obtained 5 ligand/receptor pairs between TAMs and 22RV1s IACS-9571 (Fig 2A), including the positive loop PCCSF1TAM and TAMEGFPC demonstrated by other researchers [20]. Combing the above findings, Fig 2B revealed the cell-cell interaction network between TAM, Treg, and 22RV1. All the enriched genes corresponding to Fig 2A were presented in S4 Table. Open in a separate window Fig 2 Inference of TAM-PC interactions with RNA-Seq data.(A) The left panel shows the RNA-seq data from the cocultured macrophage and PC LnCap and 22RV1 cells. Prostate cancer cells (LNCaP or 22RV1) were co-cultured with or without M2 macrophage (TAM) for 48 h and FLJ31945 RNA samples were collected for RNA-seq analysis. All of the gene expression data (fold change value) were normalized with non-co-cultured counterpart cells. For example, LNCaP W/WO TAM shows the gene expression ratio of LNCaP cells co-cultured with TAM to LNCaP cells not co-cultured with TAM. The top-ranked overexpressed genes with FC>1.3 are presented. Five enriched ligand-receptor pairs were highlighted. (B) The inferred cell-cell interaction networks between TAM, Treg, 22RV1. Taken together, our analyses show that two potential cell-cell interaction loops appear to involve in the development of CRPC. The first loop is the IACS-9571 secreted WNT5A from Tregs and macrophages triggers the activation of signaling pathways of cell survival and proliferation (e.g., WNT5A signaling, PI3K/AKT/AR and MAPK pathways, etc.) in androgen-resistant PCa cells. TRAIL IACS-9571 secreted from PCs promotes Treg proliferation [32]. The second loop is ADT-induced CSF1 expression in the tumor cells stimulates TAM.