Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model

Toxicol Appl Pharmacol. 2021 Feb 1;412:115390. doi: 10.1016/j.taap.2020.115390. Epub 2020 Dec 31.


The kidneys are metabolically active organs with importance in several physiological tasks such as the secretion of soluble wastes into the urine and synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the kidneys becomes altered. Here, we define metabolic tasks in a computational modeling framework to capture kidney function in an update to the iRno network reconstruction of rat metabolism using literature-based evidence. To demonstrate the utility of iRno for predicting kidney function, we exposed primary rat renal proximal tubule epithelial cells to four compounds with varying levels of nephrotoxicity (acetaminophen, gentamicin, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six and twenty-four hours, and collected transcriptomics and metabolomics data to measure the metabolic effects of compound exposure. For the transcriptomics data, we observed changes in fatty acid metabolism and amino acid metabolism, as well as changes in existing markers of kidney function such as Clu (clusterin). The iRno metabolic network reconstruction was used to predict alterations in these same pathways after integrating transcriptomics data and was able to distinguish between select compound-specific effects on the proximal tubule epithelial cells. Genome-scale metabolic network reconstructions with coupled omics data can be used to predict changes in metabolism as a step towards identifying novel metabolic biomarkers of kidney function and dysfunction.

Keywords: Kidney; Kidney Metabolism; Metabolic Modeling; Metabolomics; Nephrotoxicity; Transcriptomics.

Publication types

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

MeSH terms

  • Acetaminophen / toxicity
  • Animals
  • Cells, Cultured
  • Databases, Genetic
  • Energy Metabolism / drug effects*
  • Energy Metabolism / genetics
  • Epithelial Cells / drug effects*
  • Epithelial Cells / metabolism
  • Epithelial Cells / pathology
  • Female
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Gentamicins / toxicity
  • Kidney Diseases / chemically induced*
  • Kidney Diseases / genetics
  • Kidney Diseases / metabolism
  • Kidney Diseases / pathology
  • Kidney Tubules, Proximal / drug effects*
  • Kidney Tubules, Proximal / metabolism
  • Kidney Tubules, Proximal / pathology
  • Metabolome / drug effects*
  • Metabolome / genetics
  • Metabolomics
  • Polychlorinated Dibenzodioxins / toxicity
  • Rats, Sprague-Dawley
  • Transcriptome / drug effects*
  • Trichloroethylene / toxicity


  • Gentamicins
  • Polychlorinated Dibenzodioxins
  • Trichloroethylene
  • Acetaminophen