Concordance between Thioacetamide-Induced Liver Injury in Rat and Human In Vitro Gene Expression Data

Abstract

The immense resources required and the ethical concerns for animal-based toxicological studies have driven the development of in vitro and in silico approaches. Recently, we validated our approach in which the expression of a set of genes is uniquely associated with an organ-injury phenotype (injury module), by using thioacetamide, a known liver toxicant. Here, we sought to explore whether RNA-seq data obtained from human cells (in vitro) treated with thioacetamide-S-oxide (a toxic intermediate metabolite) would correlate across species with the injury responses found in rat cells (in vitro) after exposure to this metabolite as well as in rats exposed to thioacetamide (in vivo). We treated two human cell types with thioacetamide-S-oxide (primary hepatocytes with 0 (vehicle), 0.125 (low dose), or 0.25 (high dose) mM, and renal tubular epithelial cells with 0 (vehicle), 0.25 (low dose), or 1.00 (high dose) mM) and collected RNA-seq data 9 or 24 h after treatment. We found that the liver-injury modules significantly altered in human hepatocytes 24 h after high-dose treatment involved cellular infiltration and bile duct proliferation, which are linked to fibrosis. For high-dose treatments, our modular approach predicted the rat in vivo and in vitro results from human in vitro RNA-seq data with Pearson correlation coefficients of 0.60 and 0.63, respectively, which was not observed for individual genes or KEGG pathways.

Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity

“…To further corroborate the relevance of cSL load to carcinogenesis, we next investigated whether carcinogen treatment in normal (noncancer) cell lines and primary cells in vitro can lead to cSL load decrease. First, we analyzed gene expression data from a recent study where human primary hepatocytes, renal tube epithelial cells, and cardiomyocytes were treated with the carcinogen and hepatotoxin thioacetamide- S -oxide ( 25 ). We computed the cSL load in each cell type after treatment versus control and found a significant decrease of cSL load only in the hepatocytes (Wilcoxon rank sum test P = 0.014; Fig.…”

“… ( A ) Box plots showing the cSL loads in control versus thioacetamide- S -oxide–treated samples in human primary hepatocytes (“liver”), renal tube epithelial cells (“kidney”), and cardiomyocytes (“heart”), using the data from ( 25 ). One-sided Wilcoxon rank-sum test P values are shown.…”

TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries

“…For a biological interpretation, we categorized the histological endpoint into their pathological responses, inflammation, degeneration, and proliferation. The gene module approach outperforms individual genes in predicting severity of histological damage ( AbdulHameed et al, 2014 ; Tawa et al, 2014 ; Te et al, 2016 ; Schyman et al, 2020b ).…”

“…However, they do not offer detail mechanistic insights, which KEGG pathways or wiki-pathways can provide ( Kanehisa and Goto, 2000 ; Martens et al, 2020 ). We have shown that the combination of our modular approach to identify key injury phenotype together with pathway analysis, provided in ToxPanel, can be useful when understanding the underlying molecular mechanisms in e.g., liver or kidney injury ( Schyman et al, 2020a ; Schyman et al, 2020b ).…”

“…AAFC and AFC can be used for predefined or custom-designed gene sets. In the application, the current default gene sets for these methods are liver- and kidney-injury modules, which are gene sets associated with specific injury phenotypes, such as liver fibrosis and kidney necrosis ( Ippolito et al, 2015 ; AbdulHameed et al, 2016 ; Te et al, 2016 ; Schyman et al, 2018 ; Schyman et al, 2019 ; Wang et al, 2019 ; Schyman et al, 2020a ; Schyman et al, 2020b ). We also offer access to the rat and human KEGG pathways, as determined using Entrez gene IDs ( Maglott et al, 2011 ).…”