Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes

Using a 3D co-culture model, we identified significant sub-type-specific changes in the gene expression, metabolic, and therapeutic sensitivity profiles of breast cancer cells in contact with cancer-associated fibroblasts (CAFs). CAF-induced gene expression signatures predicted clinical outcome and immune-related differences in the microenvironment. We found that CAFs strongly protect carcinoma cells from lapatinib, attributable to its reduced accumulation in carcinoma cells and an elevated apoptotic threshold. Using synthetic lethality approaches, we identified molecular pathways whose inhibition sensitizes HER2+ breast cancer cells to lapatinib both in vitro and in vivo including JAK2/STAT3 and hyaluronic acid. Neoadjuvant lapatinib therapy in HER2+ breast tumors lead to a significant increase of phospho-STAT3+ cancer cells and a decrease in the spatial proximity of proliferating (Ki67+) cells to CAFs impacting therapeutic responses. Our studies identify CAF-induced physiologically and clinically relevant changes in cancer cells and offer novel approaches for overcoming microenvironment-mediated therapeutic resistance. SAGE-Seq: Differential expression analysis of five different cell lines (MCF10DCIS, SUM149PT, MCF7, T47D, and MDA-MB-453) representing three different breast cancer sub-types (triple-negative, luminal estrogen receptor positive, and HER2 positive) that were cultured in the presence and absence of cancer-associated fibroblasts (CAFs). RNA-Seq: Differential expression analysis of stromal fibroblast cells from different origins (primary breast tumors, normal breast tissue, and brain metastases of breast cancer).