Single cell RNA sequencing identifies YAP1-dependent hepatic mesothelial progenitors in fibrolamellar carcinoma

Abstract Fibrolamellar carcinoma (FLC) is characterized by in-frame fusion of DNAJB1 with PRKACA and by dense desmoplasia. Surgery is the only effective treatment, since mechanisms supporting tumor survival are unknown. We used single cell RNA-sequencing to characterize a patient-derived FLC xenograft model and identify therapeutic targets. Human FLC cells segregated into four discrete clusters that all expressed the oncogene YAP1. The two communities most enriched with cells co-expressing FLC markers (CD68, AKAP12, KRT7, EPCAM, and CPS1) also had the most cells expressing YAP1 and its pro-proliferative target genes (AREG, CCND1), suggesting these were proliferative FLC cell clusters. The other two clusters were enriched with cells expressing profibrotic YAP1 target genes, ACTA2, ELN, and COL1A1, indicating these were fibrogenic FLC cells. All clusters expressed the YAP1 target gene and mesothelial progenitor marker MSLN, and many MSLN(+) cells co-expressed albumin. Trajectory analysis predicted that the four FLC communities were derived from a single cell type transitioning among phenotypic states. After establishing a novel FLC cell line that harbored the DNAJB1-PRKACA fusion, YAP1 was inhibited, which significantly reduced expression of known YAP1-target genes as well as cell growth and migration. Thus, both FLC epithelial and stromal cells appear to arise from DNAJB1-PRKACA fusion in a YAP1-dependent liver mesothelial progenitor, identifying YAP1 as a target for FLC therapy.