Differential control of growth and identity by HNF4a isoforms in pancreatic ductal adenocarcinoma [ChIP-Seq]

Although transcriptomic studies have stratified pancreatic ductal adenocarcinoma (PDAC) into clinically relevant subtypes, classical or basal-like, further research is needed to identify the transcriptional regulators of each subtype. Previous studies identified HNF4a as a key regulator of the classical subtype, but the distinct contributions of its isoforms (P1 and P2), which display dichotomous functions in normal development and gastrointestinal malignancies, remain unexplored. Here we show that HNF4a-positive human PDAC tumors exhibit uniform expression of P2-isoforms but variable expression of P1 isoforms. To dissect the roles of each isoform in PDAC, we performed functional, transcriptomic, and epigenetic analysis after exogenous expression in HNF4a-negative models or CRISPRi-mediated knockdown of endogenous isoforms. We demonstrated that P1 isoforms are less compatible with growth and stronger transcriptional regulators than P2. Despite both isoforms sharing a common DNA binding domain, P1 isoforms displayed stronger binding at HNF4a target genes, resulting in increased transcriptional activity. These findings provide a detailed characterization of HNF4a P1 and P2 isoforms and their distinct roles in PDAC biology. Overall design: ChIPSeq was performed on human PDAC cell lines after genetic manipulation of HNF4a. BxPC3 and Panc10.05 was treated with doxycycline to induce expression of HNF4a P1 and P2 isoforms. CRISPRi was used to inhibit expression of HNF4a P1, P2, or both isoforms.