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Updated: Jul 9, 2025
Human Liver Microphysiological System for Assessing Drug-Induced Liver Toxicity In Vitro
Published on: January 31, 2022
A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying
Lukas S Wijaya1, Attila Gabor2,3, Iris E Pot1
1Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands.
Abstract:
Drug-induced liver injury (DILI) remains the main reason for drug development attritions largely due to poor mechanistic understanding. Toxicogenomic to interrogate the mechanism of DILI has been broadly performed. Gene coregulation network-based transcriptome analysis is a bioinformatics approach that potentially contributes to improve mechanistic interpretation of toxicogenomic data. Here we performed an extensive concentration time course response-toxicogenomic study in the HepG2 cell line exposed to 20 DILI compounds, 7 reference compounds for stress response pathways, and 10 agonists for cytokines and growth factor receptors. We performed whole transcriptome targeted RNA sequencing to more than 500 conditions and applied weighted gene coregulated network analysis to the transcriptomics data followed by the identification of gene coregulated networks (modules) that were strongly modulated upon the exposure of DILI compounds. Preservation analysis on the module responses of HepG2 and PHH demonstrated highly preserved adaptive stress response gene coregulated networks. We correlated gene coregulated networks with cell death onset and causal relationships of 67 critical target genes of these modules with the onset of cell death was evaluated using RNA interference screening. We identified GTPBP2, HSPA1B, IRF1, SIRT1, and TSC22D3 as essential modulators of DILI compound-induced cell death. These genes were also induced by DILI compounds in PHH. Altogether, we demonstrate the application of large transcriptome datasets combined with network-based analysis and biological validation to uncover the candidate determinants of DILI.
Insights
Drug-induced liver injury (DILI) mechanisms were explored using toxicogenomics and network analysis. Key genes like GTPBP2 and HSPA1B were identified as critical modulators of DILI-induced cell death.
Area of Science:
- Toxicogenomics
- Bioinformatics
- Molecular Toxicology
Background:
- Drug-induced liver injury (DILI) is a major cause of drug development failure due to limited mechanistic understanding.
- Toxicogenomic approaches are crucial for elucidating DILI mechanisms.
- Gene co-regulation network analysis offers a powerful bioinformatics tool for interpreting toxicogenomic data.
Purpose of the Study:
- To investigate the mechanisms of DILI using a comprehensive toxicogenomic approach.
- To identify gene co-regulated networks modulated by DILI compounds.
- To validate candidate genes involved in DILI-induced cell death.
Main Methods:
- Exposure of HepG2 cells to 20 DILI compounds and other reference chemicals.
- Whole transcriptome targeted RNA sequencing across over 500 conditions.
- Weighted gene co-regulated network analysis and RNA interference screening.
Main Results:
- Highly preserved adaptive stress response gene co-regulated networks were identified between HepG2 cells and primary human hepatocytes (PHH).
- Correlation of gene networks with cell death onset revealed critical target genes.
- GTPBP2, HSPA1B, IRF1, SIRT1, and TSC22D3 were identified as essential modulators of DILI-induced cell death, also observed in PHH.
Conclusions:
- Network-based analysis of large transcriptome datasets combined with biological validation can uncover key determinants of DILI.
- Identified genes represent potential therapeutic targets or biomarkers for DILI.
- This study advances the mechanistic understanding of DILI, aiding drug development safety.
