Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer

We performed single-cell RNA sequencing (scRNA-seq) to analyze the immune microenvironment at both the natural metastatic site in the lung and a synthetic metastatic site within a biomaterial implant (scaffold) using the 4T1 murine model of metastatic triple-negative breast cancer. Lungs, spleens, and biomaterial scaffold implants were isolated from both time-matched healthy, and 4T1-tumor bearing mice receiving throughout the normal course of metastatic progression - 7, 14, and 21 days post 4T1-inoculation. Lungs, spleens, and scaffolds were processed into a single cell suspension and analyzed by scRNAseq following standard DropSeq protocols.