Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells

Patricio Godoy, Wolfgang Schmidt-Heck, Karthick Natarajan, Balta Lucendo Villarin, Dagmara Szkolnicka, Annika Asplund, Petter Bjorquist, Agata Widera, Regina Stoeber, Gisela Campos, Seddik Hammad, Agapios Sachinidis, Umesh Chaudhari, Georg Damm, Thomas S. Weiss, Andreas K Nussler, Jane Synnergren, Karolina Edlund, Barbara Küppers-Munther, David C. HayJan G. Hengstler

Research output: Contribution to journalArticlepeer-review


Background & aims: The differentiation of stem cells to hepatocyte-like cells (HLC) offers the perspective of unlimited supply of human hepatocytes. However, the degree of differentiation of HLC remains controversial. To obtain an unbiased characterization, we performed a transcriptomics study with HLC derived from human embryonic and induced stem cells (ESC, hiPSC) from three different laboratories.
Methods: Genome-wide gene expression profiles of ESC and HLC were compared to freshly isolated and up to 14 days cultivated primary human hepatocytes. Gene networks representing successful and failed hepatocyte differentiation, and the transcription factors (TF) involved in their regulation were identified.
Results: Gene regulatory network analysis demonstrated that HLC represent a mixed cell type with features of liver, intestine, fibroblast and stem cells. The “unwanted” intestinal features were associated with KLF5 and CDX2 transcriptional networks. Cluster analysis identified highly correlated groups of genes associated with mature liver functions (n=1,057) and downregulated proliferation-associated genes (n=1,562) that approach levels of primary hepatocytes. However, three further clusters containing 447, 101 and 505 genes failed to reach levels of hepatocytes. Key TF of two of these clusters include SOX11, FOXQ1 and YBX3. The third unsuccessful cluster, controlled
by HNF1, CAR, FXR and PXR, strongly overlaps with genes repressed in cultivated
hepatocytes compared to freshly isolated hepatocytes, suggesting that current in vitro conditions lack stimuli required to maintain gene expression in hepatocytes, which consequently also explains a corresponding deficiency of HLC.
Conclusions: The present gene regulatory network approach identifies key
transcription factors for interventions to improve HLC differentiation.
Original languageEnglish
Pages (from-to)934-942
Number of pages9
JournalJournal of Hepatology
Issue number4
Early online date25 May 2015
Publication statusPublished - 1 Oct 2015


  • Stem cells
  • hepatocytes
  • differentiation
  • gene array
  • bioinformatics
  • transcriptomics
  • gene networks

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