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J Hepatol. 2015 Oct;63(4):934-42. doi: 10.1016/j.jhep.2015.05.013. Epub 2015 May 25.

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

Author information

1
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.
2
Leibniz Institute for Natural Product Research and Infection Biology eV-Hans-Knöll Institute, Jena, Germany.
3
University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), Robert-Koch-Str. 39, 50931 Cologne, Germany.
4
MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom.
5
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.
6
NovaHep AB, Arvid Wallgrens Backe 20, 41346 Gothenburg, Sweden.
7
IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.
8
Charité University Medicine Berlin, Department of General-, Visceral- and Transplantation Surgery, D13353 Berlin, Germany.
9
Center for Liver Cell Research, Department of Pediatrics and Juvenile Medicine, University of Regensburg Hospital, Regensburg, Germany.
10
Eberhard Karls University Tübingen, BG Trauma Center, Siegfried Weller Institut, D72076 Tübingen, Germany.
11
Systems Biology Research Center, School of Bioscience, University of Skövde, Sweden.
12
Takara Bio Europe AB (former Cellartis AB), Arvid Wallgrens Backe 20, 41346 Gothenburg, Sweden.
13
MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom. Electronic address: davehay@talktalk.net.
14
IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany. Electronic address: Hengstler@ifado.de.

Abstract

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 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.

KEYWORDS:

Bioinformatics; Differentiation; Gene array; Gene networks; Hepatocytes; Stem cells; Transcriptomics

PMID:
26022688
PMCID:
PMC4580233
DOI:
10.1016/j.jhep.2015.05.013
[Indexed for MEDLINE]
Free PMC Article

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