GSE159493
Dysregulation of transcription factor activity during formation of cancer associated fibroblasts.
Introduction: The reciprocal interactions between cancer cells and the CAFs serve an important role in cancer progression. Those feedback loops depend on tumor developmental stage and the tissue microenvironment and may promote different CAFs subpopulations in different types of malignancy. Here, we investigated the activation of transcription factors (TFs) in cocultures of fibroblasts with normal prostate or tumorous cells with mRNA sequencing. Materials and Methods: Coculture of WPMY-1 (normal prostate fibroblasts) with RWPE-1 (normal prostate epithelial cells) or RWPE-2 (cancer prostate epithelial cells) were done using transwell inserts. As a control, we used WPMY-1 culture alone. After 6h and 24h of coculture, we performed mRNA-sequencing., We used SEPIRA (Systems EPigenomics Inference of Regulatory Activity) package and mRNA-seq data of 483 cultured fibroblasts from GTEx to calculate the TFs activity score from mRNA-seq expression in our samples. Results: We determined changes in TFs activity between time points in each group. We found 5 TFs (RUFY3, SCMH1, NFIX, ZBTB25, NFE2L1), that increase activity between 6h and 24h in each condition (control, coculture with RWPE1 and coculture with RWPE2). Only one TF (RNF4) increased activity in RWPE-1 coculture, while dysregulation of 45 TFs (7 decreased activity and 38 increased activity) was observed in coculture with RWPE-2. Pathway analysis showed that these 45 dysregulated TFs in fibroblasts after coculture with RWPE2 cells may be associated with RUNX1 and PTEN pathways. Conclusion: Our results demonstrate that CAFs transformation can be orchestrated by dysregulation of multiple TFs, therefore may suggest multiple signaling pathways that participate in CAFs transformation. Moreover, we show potential pathways, that could be involved in feedback loop between fibroblast and epithelial cells in tumors. Overall design: mRNA profiles of WPMY-1 cocultured with RWPE-1 or RWPE-2 after 6 and 24 hours of incubation