Multiomics analysis of differentiating human cholangiocyte organoids

We aim to uncover the molecular mechanisms driving liver cellular plasticity in human chronic liver disease. We first derived intrahepatic cholangiocytes organoids (ICOs). The resulting organoid lines were then differentiated into biphenotypic cells expressing hepatocytes markers mimicking a process occurring during chronic injury in vivo. We then utilised multi-omics single nuclei RNA sequencing (snRNAseq) and assased for transcriptomics signatures and transposase-accessible chromatin (ATAC) expression to uncover the molecular pathways and the epigenetic regulations required for the in vitro conversion of cholangiocytes into hepatocytes.These analyses allowed for the identification of transcription factors involved in this process. Our analysis also suggested transdifferentiation could represent the main process by which hepatocytes are produced during liver regeneration. Overall design: To achieve our aims we used human explant liver tissue to generate organoids. These organoids were grown under cholangiocyte in vitro conditions and then switched into hepatocyte differentiation media. This process was analysed using snRNAseq and snATACseq. The molecular pathways identified relevant to the transdifferentiation were validated in vitro and in vivo using a corresponding human RNAsequencing database.