The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes

To understand the mechanisms regulating the in vitro maturation of hPSC-derived hepatocytes, we developed a 3D differentiation system and compared gene regulatory elements in human primary hepatocytes with those in hPSC-hepatocytes that were differentiated in 2D or 3D conditions by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Regulome comparisons showed a reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and active enhancers without a reduced transcription of THRB. The addition of thyroid hormone T3 increased the binding of THRB to the CYP3A4 proximal enhancer, restored the super-enhancer status and gene expression of NFIC, and reduced the expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status, and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the hPSC-hepatocytes resulted in the engraftment of human hepatocytes into the mouse liver without disrupting normal liver histology. This work implicates the environmental factor-nuclear receptor axis in regulating the maturation of hPSC-hepatocytes. [Display omitted] •THRB motif enrichment in regulomes is lower in PSC-hepatocytes than in primary hepatocytes•THRB regulates CYP3A4 expression by binding to the proximal enhancer of CYP3A4•The pBAF component PBRM1 binds THRB and is required for THRB regulation of CYP3A4•T3 promotes maturation and engraftment of in vitro differentiated hPSC-hepatocytes By developing a 3D spheroid system for hPSC-hepatocytes differentiation and combining it with genomic approaches, Jaenisch and colleagues identified a role for THRB in regulating hPSC-hepatocytes maturation through chromatin-remodeling complex pBAF. The differentiated hPSC-hepatocytes engraft into non-damaged mouse liver and proliferate in vitro in response to liver regeneration signals.