Gene expression profile at single cell level of breast cancer cells or stromal cells from a 3D culture model and cells forming mammary tumor in mouse breast cancer model

Single-cell transcriptomics to investigate shows a reprogramming of awakened cancer cells including several survival cues such as stemness, chemoresistance, as well as an altered tumor microenvironment with augmented pro-tumor immune signaling. IL-6 plays a role in cancer cell proliferation, whereas G-CSF mediates tumor immunosuppression. Pathways and differential expression analyses confirmed MEK as the key regulatory molecule in cancer cell outgrowth and survival. For 3D in vitro experiments, we isolated cancer cells and/or stromal cells with or without chemotherapy and analyzed using scRNAseq. For in vivo experiments, we harvested and digested the mammary fat pad (mfp) or mammary tumors isolated from mice treated with vehicle or docetaxel (DTX) and analyzed using scRNAseq.