Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies

A compelling body of research has confirmed the critical role of the tumor microenvironment (TME) in the growth and aggressiveness of breast cancer (BC). Cancer-associated fibroblasts (CAF), the predominant cell component of the TME, significantly influences its behavior through complex crosstalk with cancer and other stromal cells in response to tumor-derived activating signals. Murine models are extensively used to investigate the mechanisms underlying CAF's role in BC progression, as they allow for the evaluation of the endogenous TME and the assessment of immune system involvement using syngeneic xenograft studies. Here, we present a set of methods for culturing BC-derived CAFs, manipulating gene expression, and evaluating their pro-tumorigenic functions using both in vitro and in vivo approaches. We also describe protocols for CAF gene expression profiling and transcriptomic analysis, alongside a computational procedure for inferring transcriptional signatures in primary tumors using publicly available bulk RNA-seq data. Additionally, we introduce a user-friendly, web-based tool for analyzing the transcriptomes of stromal and epithelial components from laser capture micro-dissected BC tumors. Ultimately, these methods can provide valuable insights into the molecular mechanisms driving CAF-tumor interactions and hold potential for identifying novel therapeutic targets.