Comparative single-cell genomics uncovers evolutionarily conserved features and therapeutic targets in triple-negative breast cancer fibroblasts

We performed scRNA-seq analysis of fibroblasts from murine and human TNBCs. We observed three CAF subtypes in mouse TNBC: two transcriptionally distinct CAFs that were found intermingled and adjacent to tumor cells, and distal CAFs that were located further away from tumor cells. All three CAFs appear to evolve from normal resident fibroblasts/pericytes by activation of Pdgf and Tgfb receptors in fibroblasts in parallel with reciprocal upregulation of ligands in tumor cells and other tumor microenvironment cells. Additionally, extracellular matrix, glycolytic and mitochondrial respiratory genes were strongly upregulated in all three CAFs. Murine pancreatic CAFs displayed matching subtypes. Human TNBCs displayed three analogous CAF subtypes, although only a subset of marker genes are conserved. Finally, the upregulation of specific extracellular matrix genes in different CAF subtypes provides a basis for developing selective CAF-targeted therapeutics. Overall design: scRNAseq was performed on a total of thirteen samples: three human samples and ten mouse samples. The human tissue samples of triple negative breast tumors were provided by the NCI Cooperative Human Tissue Network. The murine breast tumor samples were harvested from mammary glands of two transgenic mouse models: a) MMTV-PyMT and b) C3(1)-Tag SV40. The pancreatic tumor came from the Ptf1?-CreERTM; LSL- KRASG12D strain. .