Abstract: Objective To explore the potential application of the intrahepatic cholangiocyte organoid (ICO) differentiation model to study liver development. Methods Combining CRISPR/Cas9 gene editing technology and ICO differentiation model, bulk RNA-seq data of the organoids cultured in expansion medium, differentiation medium, and differentiation medium after Hnf4α knockout were used to analyze the transdifferentiation process of ICO, and public single-cell transcriptome data sets were used to analyze the differentiation during fetal liver development. The two differentiation processes were compared in three aspects: the change of gene expression, biological function, and transcriptional regulation taking Hnf4α regulon as an example. Results The change of gene expression during ICO transdifferentiation was almost consistent with that in liver development. The up-regulated genes during transdifferentiation were mainly enriched in metabolism-related pathways closely associated biological functions of liver parenchymal cells. The downstream target genes of Hnf4α during ICO transdifferentiation were overlapped with those in fetal liver development. Conclusions ICO transdifferentiation model can partially simulate the differentiation process of fetal liver development.

Key words: intrahepatic cholangiocyte organoid, RNA-seq, differentiation, hepatocyte nuclear factor 4α(Hnf4α)