Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes

Toxicol Sci. 2019 Dec 1;172(2):279-291. doi: 10.1093/toxsci/kfz197.


Context-specific GEnome-scale metabolic Network REconstructions (GENREs) provide a means to understand cellular metabolism at a deeper level of physiological detail. Here, we use transcriptomics data from chemically-exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism and predict biomarkers of liver toxicity using the Transcriptionally Inferred Metabolic Biomarker Response algorithm. We profiled alterations in cellular hepatocyte metabolism following in vitro exposure to four toxicants (acetaminophen, carbon tetrachloride, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six hour. TIMBR predictions were compared with paired fresh and spent media metabolomics data from the same exposure conditions. Agreement between computational model predictions and experimental data led to the identification of specific metabolites and thus metabolic pathways associated with toxicant exposure. Here, we identified changes in the TCA metabolites citrate and alpha-ketoglutarate along with changes in carbohydrate metabolism and interruptions in ATP production and the TCA Cycle. Where predictions and experimental data disagreed, we identified testable hypotheses to reconcile differences between the model predictions and experimental data. The presented pipeline for using paired transcriptomics and metabolomics data provides a framework for interrogating multiple omics datasets to generate mechanistic insight of metabolic changes associated with toxicological responses.

Keywords: constraint-based modeling; metabolism; metabolomics; toxicology; transcriptomics.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetaminophen / toxicity
  • Activation, Metabolic / drug effects*
  • Activation, Metabolic / genetics
  • Animals
  • Biomarkers / metabolism
  • Carbon Tetrachloride / toxicity
  • Cells, Cultured
  • Computational Biology
  • Gene Expression Profiling
  • Hepatocytes / drug effects*
  • Hepatocytes / metabolism*
  • Male
  • Metabolic Networks and Pathways / drug effects*
  • Metabolic Networks and Pathways / genetics
  • Metabolomics
  • Polychlorinated Dibenzodioxins / toxicity
  • Primary Cell Culture
  • Rats, Sprague-Dawley
  • Transcriptome / drug effects*
  • Trichloroethylene / toxicity


  • Biomarkers
  • Polychlorinated Dibenzodioxins
  • Trichloroethylene
  • Acetaminophen
  • Carbon Tetrachloride