Comparative transcriptomics of hepatic differentiation of human pluripotent stem cells and adult human liver tissue.

Nidal Ghosheh,Barbara Küppers-Munther,Tommy B Andersson,Christian X Andersson,Peter Sartipy,Josefina Edsbagge,Benjamin Ulfenborg,Stina Simonsson,Helena Carén,Petter Björquist,Annika Asplund,Jane Synnergren

doi:10.1152/physiolgenomics.00007.2017

Abstract

Hepatocytes derived from human pluripotent stem cells (hPSC-HEP) have the potential to replace presently used hepatocyte sources applied in liver disease treatment and models of drug discovery and development. Established hepatocyte differentiation protocols are effective and generate hepatocytes, which recapitulate some key features of their in vivo counterparts. However, generating mature hPSC-HEP remains a challenge. In this study, we applied transcriptomics to investigate the progress of in vitro hepatic differentiation of hPSCs at the developmental stages, definitive endoderm, hepatoblasts, early hPSC-HEP, and mature hPSC-HEP, to identify functional targets that enhance efficient hepatocyte differentiation. Using functional annotation, pathway and protein interaction network analyses, we observed the grouping of differentially expressed genes in specific clusters representing typical developmental stages of hepatic differentiation. In addition, we identified hub proteins and modules that were involved in the cell cycle process at early differentiation stages. We also identified hub proteins that differed in expression levels between hPSC-HEP and the liver tissue controls. Moreover, we identified a module of genes that were expressed at higher levels in the liver tissue samples than in the hPSC-HEP. Considering that hub proteins and modules generally are essential and have important roles in the protein-protein interactions, further investigation of these genes and their regulators may contribute to a better understanding of the differentiation process. This may suggest novel target pathways and molecules for improvement of hPSC-HEP functionality, having the potential to finally bring this technology to a wider use.

Highlights

LIVER DISEASE ACCOUNTS for the death of ~1.7 million patients worldwide yearly [50], hereby becoming one of the leading cause of mortality in the world [34, 43, 49]
The dendrogram confirms that the later differentiation stages show higher similarity to each other than to the earlier stages such as definitive endoderm (DE) cells and Human pluripotent stem cells (hPSCs)
Higher in the dendrogram, the human liver samples cluster with the later differentiation stages, as expected

Summary

Introduction

LIVER DISEASE ACCOUNTS for the death of ~1.7 million patients worldwide yearly [50], hereby becoming one of the leading cause of mortality in the world [34, 43, 49]. HPSCs have successfully been differentiated into hepatocytes (hPSC-HEP), sharing many features with in vivo hepatocytes, such as cytochrome P450 enzyme activity and glycogen storage, in addition to expression of several drug transporters [1, 17, 18, 52, 58]. They are applicable for long-term toxicity studies [21] and can accurately classify toxic agents [55]. HPSC-HEP were shown to recapitulate important functionality of their in vivo counterparts, such as cytochrome P450 enzyme activity comparable to freshly isolated hepatocytes, expression of several drug transporters, and glycogen storage. Hub proteins [proteins with high level of interactivity that usually are essential and play central role in protein interaction networks [53]], which appear to be involved in the different hepatocyte developmental stages, were identified

Methods

Results

Conclusion