A Network-based Transcriptomic Landscape of HepG2 cells to Uncover Causal Gene Cytotoxicity Interactions Underlying Drug-Induced Liver Injury

Drug-induced liver injury (DILI) remains the main reason of drug development attritions largely due to poor mechanistic understanding. Toxicogenomics to interrogate the mechanism of DILI has been broadly performed. Gene network-based transcriptome analysis is a bioinformatics approach that potentially contributes to improving mechanistic interpretation of toxicogenomics data. In this current study, we performed an extensive concentration time course response-toxicogenomics study in the HepG2 cell line exposed to various DILI compounds, reference compounds for stress response pathways, cytokine receptors, and growth factor receptors. We established > 500 conditions subjected to whole transcriptome targeted RNA sequences and applied weighted gene co-regulated network analysis (WGCNA) to the transcriptomics data followed by identification of gene 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 responses gene networks. We correlated gene network with cell death as the progressive cellular outcomes. Causality of the target genes of these modules was evaluated using RNA interference validation experiments. We identified that GTPBP2, HSPA1B, IRF1, SIRT1 and TSC22D3 exhibited strong causality towards cell death. Altogether, we demonstrate the application of large transcriptome datasets combined with network-based analysis and biological validation to uncover the candidate determinants of DILI.