A framework for large-scale metabolome drug profiling links coenzyme A metabolism to the toxicity of anti-cancer drug dichloroacetate

Sébastien Dubuis,Karin Ortmayr,Mattia Zampieri

doi:10.1038/s42003-018-0111-x

Abstract

Metabolic profiling of cell line collections has become an invaluable tool to study disease etiology, drug modes of action and to select personalized treatments. However, large-scale in vitro dynamic metabolic profiling is limited by time-consuming sampling and complex measurement procedures. By adapting a mass spectrometry-based metabolomics workflow for high-throughput profiling of diverse adherent mammalian cells, we establish a framework for the rapid measurement and analysis of drug-induced dynamic changes in intracellular metabolites. This methodology is scalable to large compound libraries and is here applied to study the mechanism underlying the toxic effect of dichloroacetate in ovarian cancer cell lines. System-level analysis of the metabolic responses revealed a key and unexpected role of CoA biosynthesis in dichloroacetate toxicity and the more general importance of CoA homeostasis across diverse human cell lines. The herein-proposed strategy for high-content drug metabolic profiling is complementary to other molecular profiling techniques, opening new scientific and drug-discovery opportunities.

Highlights

Metabolic profiling of cell line collections has become an invaluable tool to study disease etiology, drug modes of action and to select personalized treatments
Applied to drug discovery research, metabolome profiling of drugperturbed cell lines in vitro was key in revealing drug modes of action and in identifying potential weaknesses in cellular drug response, as well as genetic polymorphisms associated with drug susceptibility[12,13,14,15,16,17,18,19]
Our group developed a high-throughput and robust method to perform large-scale metabolic profiling in adherent mammalian cells at steady state[26], using a 96-well plate cultivation format combined with time-lapse microscopy and flow-injection time-of-flight mass spectrometry[23] (TOFMS)

Summary

Introduction

Metabolic profiling of cell line collections has become an invaluable tool to study disease etiology, drug modes of action and to select personalized treatments. Metabolome screenings that adopt classical metabolomics techniques[24,25] are often hampered by a limited throughput, laborious sample preparation and the lack of rigorous, yet simple, data analysis pipelines to interpret dynamic metabolome profiles To address these limitations, our group developed a high-throughput and robust method to perform large-scale metabolic profiling in adherent mammalian cells at steady state[26], using a 96-well plate cultivation format combined with time-lapse microscopy and flow-injection time-of-flight mass spectrometry[23] (TOFMS). Our group developed a high-throughput and robust method to perform large-scale metabolic profiling in adherent mammalian cells at steady state[26], using a 96-well plate cultivation format combined with time-lapse microscopy and flow-injection time-of-flight mass spectrometry[23] (TOFMS) We extend this methodology to allow rapid sample collection and the analysis of dynamic changes in the intracellular metabolome of diverse mammalian cell lines upon external perturbations. In absence of prior chromatographic separation, FIA-TOFMS cannot distinguish isobaric metabolites, as well as in-source fragments that are detected at the identical exact mass

Methods

Results

Conclusion