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. Hay; Jan G.  Hengstler

doi:10.1016/j.jhep.2015.05.013

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 journal › Article › peer-review

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 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 language	English
Pages (from-to)	934-942
Number of pages	9
Journal	Journal of Hepatology
Volume	63
Issue number	4
Early online date	25 May 2015
DOIs	https://doi.org/10.1016/j.jhep.2015.05.013
Publication status	Published - 1 Oct 2015

Keywords / Materials (for Non-textual outputs)

Stem cells
hepatocytes
differentiation
gene array
bioinformatics
transcriptomics
gene networks

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10.1016/j.jhep.2015.05.013

JHEPAT-D-15-00509R1Accepted author manuscript, 577 KB
Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells
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http://www.sciencedirect.com/science/article/pii/S0168827815003402

The development of 3-dimensional implantable liver organoids
Callanan, A. (Principal Investigator)
MRC
1/10/14 → 10/04/18
Project: Research
The development of 3-dimensional implantable liver organoids
Hay, D. (Principal Investigator)
MRC
1/10/14 → 10/04/18
Project: Research
A HUB FOR ENGINEERING AND EXPLOITING THE STEM CELL NICHE
Forbes, S. (Principal Investigator)
MRC
1/11/13 → 31/03/18
Project: Research

David Hay
- Deanery of Clinical Sciences - Personal Chair of Tissue Engineering
Person: Academic: Research Active

Cite this

Godoy, P., Schmidt-Heck, W., Natarajan, K., Lucendo Villarin, B., Szkolnicka, D., Asplund, A., Bjorquist, P., Widera, A., Stoeber, R., Campos, G., Hammad, S., Sachinidis, A., Chaudhari, U., Damm, G., Weiss, T. S., Nussler, A. K., Synnergren, J., Edlund, K., Küppers-Munther, B., ... Hengstler, J. G. (2015). Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells. Journal of Hepatology, 63(4), 934-942. https://doi.org/10.1016/j.jhep.2015.05.013

@article{a0e79f95f266430286132118bef50743,

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

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 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, controlledby HNF1, CAR, FXR and PXR, strongly overlaps with genes repressed in cultivatedhepatocytes 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 keytranscription factors for interventions to improve HLC differentiation.",

keywords = "Stem cells, hepatocytes, differentiation, gene array, bioinformatics, transcriptomics, gene networks",

author = "Patricio Godoy and Wolfgang Schmidt-Heck and Karthick Natarajan and {Lucendo Villarin}, Balta and Dagmara Szkolnicka and Annika Asplund and Petter Bjorquist and Agata Widera and Regina Stoeber and Gisela Campos and Seddik Hammad and Agapios Sachinidis and Umesh Chaudhari and Georg Damm and Weiss, {Thomas S.} and Nussler, {Andreas K} and Jane Synnergren and Karolina Edlund and Barbara K{\"u}ppers-Munther and Hay, {David C.} and Hengstler, {Jan G.}",

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doi = "10.1016/j.jhep.2015.05.013",

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Godoy, P, Schmidt-Heck, W, Natarajan, K, Lucendo Villarin, B, Szkolnicka, D, Asplund, A, Bjorquist, P, Widera, A, Stoeber, R, Campos, G, Hammad, S, Sachinidis, A, Chaudhari, U, Damm, G, Weiss, TS, Nussler, AK, Synnergren, J, Edlund, K, Küppers-Munther, B, Hay, DC & Hengstler, JG 2015, 'Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells', Journal of Hepatology, vol. 63, no. 4, pp. 934-942. https://doi.org/10.1016/j.jhep.2015.05.013

TY - JOUR

T1 - Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells

AU - Godoy, Patricio

AU - Schmidt-Heck, Wolfgang

AU - Natarajan, Karthick

AU - Lucendo Villarin, Balta

AU - Szkolnicka, Dagmara

AU - Asplund, Annika

AU - Bjorquist, Petter

AU - Widera, Agata

AU - Stoeber, Regina

AU - Campos, Gisela

AU - Hammad, Seddik

AU - Sachinidis, Agapios

AU - Chaudhari, Umesh

AU - Damm, Georg

AU - Weiss, Thomas S.

AU - Nussler, Andreas K

AU - Synnergren, Jane

AU - Edlund, Karolina

AU - Küppers-Munther, Barbara

AU - Hay, David C.

AU - Hengstler, Jan G.

PY - 2015/10/1

Y1 - 2015/10/1

N2 - 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, controlledby HNF1, CAR, FXR and PXR, strongly overlaps with genes repressed in cultivatedhepatocytes 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 keytranscription factors for interventions to improve HLC differentiation.

AB - 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, controlledby HNF1, CAR, FXR and PXR, strongly overlaps with genes repressed in cultivatedhepatocytes 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 keytranscription factors for interventions to improve HLC differentiation.

KW - Stem cells

KW - hepatocytes

KW - differentiation

KW - gene array

KW - bioinformatics

KW - transcriptomics

KW - gene networks

U2 - 10.1016/j.jhep.2015.05.013

DO - 10.1016/j.jhep.2015.05.013

M3 - Article

SN - 0168-8278

VL - 63

SP - 934

EP - 942

JO - Journal of Hepatology

JF - Journal of Hepatology

IS - 4

ER -

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

Abstract

Keywords / Materials (for Non-textual outputs)

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Projects

The development of 3-dimensional implantable liver organoids

The development of 3-dimensional implantable liver organoids

A HUB FOR ENGINEERING AND EXPLOITING THE STEM CELL NICHE

Profiles

David Hay

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