TY - JOUR
T1 - Comparing in vitro human liver models to in vivo human liver using RNA-Seq
AU - Gupta, Rajinder
AU - Schrooders, Yannick
AU - Hauser, Duncan
AU - van Herwijnen, Marcel
AU - Albrecht, Wiebke
AU - ter Braak, Bas
AU - Brecklinghaus, Tim
AU - Castell, Jose V.
AU - Elenschneider, Leroy
AU - Escher, Sylvia
AU - Guye, Patrick
AU - Hengstler, Jan G.
AU - Ghallab, Ahmed
AU - Hansen, Tanja
AU - Leist, Marcel
AU - Maclennan, Richard
AU - Moritz, Wolfgang
AU - Tolosa, Laia
AU - Tricot, Tine
AU - Verfaillie, Catherine
AU - Walker, Paul
AU - van de Water, Bob
AU - Kleinjans, Jos
AU - Caiment, Florian
N1 - Funding Information:
This work was supported by the EU-ToxRisk project (An Integrated European “Flagship” Program Driving Mechanism-Based Toxicity Testing and Risk Assessment for the 21st Century) funded by the European Commission under the Horizon 2020 program (Grant Agreement No. 681002). L.T. was supported by the Institute of Health Carlos III (Plan Estatal de I + D + i 2013–2016) and co-financed by the European Regional Development Fund “A way to achieve Europe” (FEDER) through grant CP16/00097.
Publisher Copyright:
© 2020, The Author(s).
PY - 2021/2
Y1 - 2021/2
N2 - The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
AB - The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
KW - In vivo liver
KW - In vitro liver
KW - RNA-seq
KW - CellNet
KW - Non-DEGs
KW - Non-DEGs(DTU)
KW - Pathway coverage
KW - HEPARG CELLS
KW - PRIMARY HEPATOCYTES
KW - TOXICITY
KW - DIFFERENTIATION
KW - HEPATOTOXICITY
KW - METABOLISM
KW - INDUCTION
KW - EVOLUTION
KW - PLATFORM
KW - SYSTEMS
U2 - 10.1007/s00204-020-02937-6
DO - 10.1007/s00204-020-02937-6
M3 - Article
C2 - 33106934
SN - 0340-5761
VL - 95
SP - 573
EP - 589
JO - Archives of Toxicology
JF - Archives of Toxicology
IS - 2
ER -