RNA-sequencing of multicellular human liver organoids derived from 3 different iPS cells

By taking advantage of the foregut generation method, we initially differentiated iPSCs to foregut spheroids through definitive endoderm specification as described. The foregut spheroids were embedded in Matrigel and cultured with retinoic acid (RA). Following 4-day RA treatment, we switched into hepatocyte maturation media for the induction of the hepatocyte differentiation process to establish human liver organoids, hereafter defined as HLO, as early as day 20. To characterize the lipid metabolism related genes in HLO, we conducted RNA sequencing to unbiasedly identify and visualize coordinately expressed gene signatures among groups of three different iPSC derived HLO, and various stage-derived primary-liver cells and tissues as previously described. Correlation spanning tree based on self-organizing maps analysis using 18,338 genes organized into 400 metagenes confirmed overall similarities between HLO and primary hepatocytes, yet distinct from human fetal liver samples. Highly comparable signatures to primary hepatocytes contained major hepatocyte associated genes including lipid metabolism, suggesting that the HLO continue to progress towards a hepatocyte-like fate. Examination of mRNA expression profile in multicellular human liver organoids derived from 3 different iPS cells