Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment

We used single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments. To investigate the architectural effects of matrix stiffness on the tumor microenvironment, we performed scRNAseq on stiff and compliant MMTV-PyMT mammary tumors. To obtain compliant and stiff tumors, MMTV-PyMT mice were treated with BAPN, a lysyl oxidase inhibitor, or vehicle control, respectively. Tumors were dissociated to form single cell suspensions and encapsulated using a custom inDrop platform. Tumors were excised, encapsulated, and sequenced pairwise in 3 batches on separate days and sequencing runs. All sequencing results were filtered using several quality control methods prior to analysis. Inflection point gating for total counts per cell was applied to each sample individually to remove cells with low library size and an upper threshold was applied to remove droplets that may have contained more than 1 cell. Additionally, cells containing a high proportion of mitochondrial genes were removed.