title: Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells.
abstract: OBJECTIVE
  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 transcriptomic 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 14days cultivated primary human hepatocytes. Gene networks representing successful and failed hepatocyte differentiation, and the transcription factors 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=1057) and downregulated proliferation associated genes (n=1562) 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 which require modulation to improve HLC differentiation.
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany; Department of Physiology, Faculty of Biological Sciences, University of Concepción, Chile.
authors.forename: Patricio
authors.initials: P
authors.lastname: Godoy
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology eV-Hans-Knöll Institute, Jena, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schmidt-Heck
authors.affiliation: University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: Karthick
authors.initials: K
authors.lastname: Natarajan
authors.affiliation: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom.
authors.forename: Baltasar
authors.initials: B
authors.lastname: Lucendo-Villarin
authors.affiliation: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom.
authors.forename: Dagmara
authors.initials: D
authors.lastname: Szkolnicka
authors.affiliation: Takara Bio Europe AB (former Cellartis AB), Arvid Wallgrens Backe 20, 41346 Gothenburg, Sweden; Systems Biology Research Center, School of Bioscience, University of Skövde, Sweden.
authors.forename: Annika
authors.initials: A
authors.lastname: Asplund
authors.affiliation: NovaHep AB, Arvid Wallgrens Backe 20, 41346 Gothenburg, Sweden.
authors.forename: Petter
authors.initials: P
authors.lastname: Björquist
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
authors.forename: Agata
authors.initials: A
authors.lastname: Widera
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: Stöber
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
authors.forename: Gisela
authors.initials: G
authors.lastname: Campos
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
authors.forename: Seddik
authors.initials: S
authors.lastname: Hammad
authors.affiliation: University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: Agapios
authors.initials: A
authors.lastname: Sachinidis
authors.affiliation: University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: Umesh
authors.initials: U
authors.lastname: Chaudhari
authors.affiliation: Charité University Medicine Berlin, Department of General-, Visceral- and Transplantation Surgery, D13353 Berlin, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Damm
authors.affiliation: Center for Liver Cell Research, Department of Pediatrics and Juvenile Medicine, University of Regensburg Hospital, Regensburg, Germany.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Weiss
authors.affiliation: Eberhard Karls University Tübingen, BG Trauma Center, Siegfried Weller Institut, D72076 Tübingen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Nüssler
authors.affiliation: Systems Biology Research Center, School of Bioscience, University of Skövde, Sweden.
authors.forename: Jane
authors.initials: J
authors.lastname: Synnergren
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
authors.forename: Karolina
authors.initials: K
authors.lastname: Edlund
authors.affiliation: Takara Bio Europe AB (former Cellartis AB), Arvid Wallgrens Backe 20, 41346 Gothenburg, Sweden.
authors.forename: Barbara
authors.initials: B
authors.lastname: Küppers-Munther
authors.affiliation: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom. Electronic address: davehay@talktalk.net.
authors.forename: David C
authors.initials: DC
authors.lastname: Hay
authors.affiliation: IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany. Electronic address: Hengstler@ifado.de.
authors.forename: Jan G
authors.initials: JG
authors.lastname: Hengstler
mesh_terms: D002454:Cell Differentiation; D002478:Cells, Cultured; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D053263:Gene Regulatory Networks; D022781:Hepatocytes / Q000166:cytology* / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism; D008099:Liver / Q000166:cytology / Q000378:metabolism*; D012313:RNA / Q000235:genetics*; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics*; D059467:Transcriptome
chemical_list: D014157:Transcription Factors; D012313:RNA
keywords: Bioinformatics; Differentiation; Gene array; Gene networks; Hepatocytes; Stem cells; Transcriptomics