Profiling chromatin accessibility of neutrophil subsets in a mouse model of pancreatic cancer [ATAC-Seq]
Neutrophils are increasingly recognized as key players in the tumour immune response, and are associated with poor clinical outcomes. Despite recent advances characterizing the diversity of neutrophil states in cancer, common trajectories and mechanisms governing the ontogeny and relationship between these neutrophil states remain undefined.Using Assay for Transposase Accessible Chromatin (ATAC) sequencing, we show that immature and mature neutrophils infiltrating the tumor share a similar chromatin accessibility profile that was not observed in non-tumor populations (in both tumor-bearing and wild type mice). Our results thus indicate that tumor-infiltrating neutrophils can be reprogrammed by the tumor microenvironment regardless of their stage of maturity by converging chromatin trajectories towards a distinct T3 state. Overall design: CD11b+CD115-Ly6G+CD101+ mature and CD101- immature neutrophils were sorted by fluorescence activated cell sorting (FACS) from the bone marrow (BM), spleen (SPL), blood (BLD) and tumor (TUM) from mice bearing orthotopic tumors previously established from the Pdx1Cre; KrasG12D/+; Trp53R172H/+ (KPC) genetically modified mouse model (n=3 for all except mature blood neutrophils, n=3). Mature and immature neutrophils from the bone marrow of wild type mice were also further sorted as controls (n=3).