A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas [scATAC-seq]

Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible. Single cell suspensions were prepared from inflammation-resolved (or control) pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube.