Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress

Anja Wilmes, Alice Limonciel, Lydia Aschauer, Konrad Moenks, Chris Bielow, Martin O Leonard, Jeremy Hamon, Donatella Carpi, Silke Ruzek, Andreas Handler, Olga Schmal, Karin Herrgen, Patricia Bellwon, Christof Burek, Germaine L Truisi, Philip Hewitt, Emma Di Consiglio, Emanuela Testai, Bas J. Blaauboer, Claude GuillouChristian G Huber, Arno Lukas, Walter Pfaller, Stefan O Mueller, Frederic Y Bois, Wolfgang Dekant, Paul Jennings

Research output: Contribution to JournalArticleAcademicpeer-review


High content omic techniques in combination with stable human in vitro cell culture systems have the potential to improve on current pre-clinical safety regimes by providing detailed mechanistic information of altered cellular processes. Here we investigated the added benefit of integrating transcriptomics, proteomics and metabolomics together with pharmacokinetics for drug testing regimes. Cultured human renal epithelial cells (RPTEC/TERT1) were exposed to the nephrotoxin Cyclosporine A (CsA) at therapeutic and supratherapeutic concentrations for 14days. CsA was quantified in supernatants and cellular lysates by LC-MS/MS for kinetic modeling. There was a rapid cellular uptake and accumulation of CsA, with a non-linear relationship between intracellular and applied concentrations. CsA at 15μM induced mitochondrial disturbances and activation of the Nrf2-oxidative-damage and the unfolded protein-response pathways. All three omic streams provided complementary information, especially pertaining to Nrf2 and ATF4 activation. No stress induction was detected with 5μM CsA; however, both concentrations resulted in a maximal secretion of cyclophilin B. The study demonstrates for the first time that CsA-induced stress is not directly linked to its primary pharmacology. In addition we demonstrate the power of integrated omics for the elucidation of signaling cascades brought about by compound induced cell stress.

Original languageEnglish
Pages (from-to)180-94
Number of pages15
JournalJournal of Proteomics
Publication statusPublished - 21 Feb 2013
Externally publishedYes


  • Cyclophilins
  • Cyclosporine
  • Epithelial Cells
  • Humans
  • Kidney Tubules, Proximal
  • Metabolomics
  • NF-E2-Related Factor 2
  • Oxidative Stress
  • Proteomics
  • Signal Transduction
  • Tandem Mass Spectrometry
  • Toxicology
  • Journal Article
  • Research Support, Non-U.S. Gov't


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