TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer [ChIP-/ATAC-seq]

In pancreatic cancer, two distinct transcriptomic subtypes were identified with a high prognostic relevance: the classical and basal-like subtype. Therefore, in this study, we wanted to use an unbiased method to investigate the global chromatin accessibility in subtype-defined pancreatic cancer cell lines, as well as define the binding profile of the highly subtype-dependent JUN/AP1 transcription factors JUNB (classical) and cJUN (basal). Hence, we performed ATAC-seq in two classical and basal-like cells, as well as ChIP-seq for JUNB in classical CAPAN1 cells and for cJUN in basal-like PANC1 cells. ChIP-seq was performed for JUNB in CAPAN1 cells, as well as for cJUN in PANC1. Two repeats were used in each group. ATAC-seq was performed in CAPAN1, CAPAN2, PANC1 and MiaPaCa2 cells. Three repeats for CAPAN1, CAPAN2, PANC1; two repeats for MiaPaCa2.