The effect of variantions in DNA methylation patterns on gene expression and functionality of hepatocytes derived from human pluripotent stem cells

Human pluripotent stem cells (hPSC) are characterized by their unique capacities of self-renewal and differentiation, and, as such, they provide an excellent human cell source in basic research, drug discovery and regenerative medicine.

Stem cells have potential to provide an unlimited source of human cells with high relevance and high reproducibility, useful in a wide range of applications. Human PSCs can be differentiated to hepatocytes but these cells have lower expression of some key genes important for their metabolic functionality, which currently limits their use for some applications in drug discovery. Variations in DNA methylation has been demonstrated upon differentiation of hPSC and these differences may underlie the functionality impairment of in vitro differentiated cells.

This project investigates how atypical methylation patterns affect the function of hepatocytes generated in vitro from hPSC, with the ultimate goal to develop differentiation regimes that prevent these defects. For this purpose DNA methylation arrays and mRNA arrays will be run on samples from defined stages during the differentiation process and will be compared to data from primary cells. By inclusion of both embryonic stem cells and induced pluripotent stem cells, reprogrammed from somatic cells, the presence of an epigenetic memory will be investigated. The project will identify key genes involved in changes in DNA methylation during differentiation towards the hepatic lineages. It will also develop methods to regulate DNA methylation through genetic and/or chemical manipulations and explore the possibility of an epigenetic memory in reprogrammed cells that are derived in vitro. Ultimately, it will pave the way for in vitro generation of hepatocytes with improved functionality that permit their application in drug development, toxicology screens and regenerative medicine.


Ghosheh N, Olsson B, Edsbagge J, Küppers-Munther B, Van Giezen M, Asplund A, Andersson TB, Björquist P, Carén H, Simonsson S, Sartipy P, Synnergren J. (2016) Highly Synchronized Expression of Lineage-Specific Genes during In Vitro Hepatic Differentiation of Human Pluripotent Stem Cell Lines. Stem Cells Int. doi: 10.1155/2016/8648356.

picture stem cells

picture stem cells

picture stem cells - By Christoph Bock (Max Planck Institute for Informatics) - Own work, CC BY-SA 3.0

By Christoph Bock (Max Planck Institute for Informatics) - Own work, CC BY-SA 3.0


Project leader

The project in short

Full name of project:
Aberrant DNA methylation patterns in hepatocytes derived from human pluripotent stem cells

2013-07-01 until 2016-06-30

Financed by:
Knowledge Foundation

Collaborating partners:
Takara Bio Europe AB
AstraZeneca AB

Researchers related to the current project

Jane Synnergren, PhD, Project leader

Nidal Ghosheh, PhD student

Annika Asplund, PhD

Peter Sartipy, Adjunct Prof.