Abstract
The chemotherapeutic compound, cisplatin causes various kinds of DNA lesions but also triggers other pertubations, such as ER and oxidative stress. We and others have shown that treatment of pluripotent stem cells with cisplatin causes a plethora of transcriptional and post-translational alterations that, to a major extent, point to DNA damage response (DDR) signaling. The orchestrated DDR signaling network is important to arrest the cell cycle and repair the lesions or, in case of damage beyond repair, eliminate affected cells. Failure to properly balance the various aspects of the DDR in stem cells contributes to ageing and cancer. Here, we performed metabolic profiling by mass spectrometry of embryonic stem (ES) cells treated for different time periods with cisplatin. We then integrated metabolomics with transcriptomics analyses and connected cisplatin-regulated metabolites with regulated metabolic enzymes to identify enriched metabolic pathways. These included nucleotide metabolism, urea cycle and arginine and proline metabolism. Silencing of identified proline metabolic and catabolic enzymes indicated that altered proline metabolism serves as an adaptive, rather than a toxic response. A group of enriched metabolic pathways clustered around the metabolite S-adenosylmethionine, which is a hub for methylation and transsulfuration reactions and polyamine metabolism. Enzymes and metabolites with pro- or anti-oxidant functions were also enriched but enhanced levels of reactive oxygen species were not measured in cisplatin-treated ES cells. Lastly, a number of the differentially regulated metabolic enzymes were identified as target genes of the transcription factor p53, pointing to p53-mediated alterations in metabolism in response to genotoxic stress. Altogether, our findings reveal interconnecting metabolic pathways that are responsive to cisplatin and may serve as signaling modules in the DDR in pluripotent stem cells.
Highlights
Metabolic changes are associated with a number of complex diseases, including cancer, diabetes and neurological disorders
General considerations - To explore intracellular metabolic changes in response to genotoxic stress in pluripotent stem cells, embryonic stem (ES) cells were treated with a sub-lethal dose of 5 mM cisplatin for 4 h and 8 h and lysates were prepared for metabolomics analysis (Fig. S1A)
By integrating metabolomics and transcriptomics analyses of cisplatin-treated ES cells, we have identified metabolic pathways that are significantly affected by the treatment with this genotoxic compound
Summary
Metabolic changes are associated with a number of complex diseases, including cancer, diabetes and neurological disorders. Mutations in a number of metabolic enzymes were recently related to inherited cancer syndromes [3]. This link between metabolism and disease suggests that metabolomics may be used to identify biomarkers suitable for noninvasive methods to determine disease state, treatment and toxic responses [4]. Irradiation or chemotherapeutic treatment alters the abundance of metabolites, including for example choline-containing compounds, lipids and several amino acids in cancer cell lines [5,6]. The NCI60 panel of tumor cells lines was used to correlate treatment response to platinum drugs with baseline metabolic pathways extracted from metabolomics and transcriptomics [8]. Integrated approaches aimed at unraveling perturbation of metabolic pathways in response to therapy are currently lacking
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