Research article

Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS coupling

Dino Bullinger^1* , Hans Neubauer^2* , Tanja Fehm² , Stefan Laufer³ , Christoph H Gleiter¹ and Bernd Kammerer¹

¹  Department of Pharmacology and Toxicology, Division of Clinical Pharmacology, University Hospital Tübingen, Otfried-Müller-Str. 45, 72076 Tübingen, Germany

²  Department of Obstetrics and Gynecology, University Hospital Tübingen, Calwerstr. 7, 72076 Tübingen, Germany

³  Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany

author email corresponding author email* Contributed equally

BMC Biochemistry 2007, 8:25doi:10.1186/1471-2091-8-25

Published:	29 November 2007

Abstract

Background

Cancer, like other diseases accompanied by strong metabolic disorders, shows characteristic effects on cell turnover rate, activity of modifying enzymes and DNA/RNA modifications, resulting also in elevated amounts of excreted modified nucleosides. For a better understanding of the impaired RNA metabolism in breast cancer cells, we screened these metabolites in the cell culture supernatants of the breast cancer cell line MCF-7 and compared it to the human mammary epithelial cells MCF-10A. The nucleosides were isolated and analyzed via 2D-chromatographic techniques: In the first dimension by cis-diol specific boronate affinity extraction and subsequently by reversed phase chromatography coupled to an ion trap mass spectrometer.

Results

Besides the determination of ribonucleosides, additional compounds with cis-diol structure, deriving from cross-linked biochemical pathways, like purine-, histidine- and polyamine metabolism were detected. In total, 36 metabolites were identified by comparison of fragmentation patterns and retention time. Relation to the internal standard isoguanosine yielded normalized area ratios for each identified compound and enabled a semi-quantitative metabolic signature of both analyzed cell lines.

13 of the identified 26 modified ribonucleosides were elevated in the cell culture supernatants of MCF-7 cells, with 5-methyluridine, N²,N²,7-trimethylguanosine, N⁶-methyl-N⁶-threonylcarbamoyladenosine and 3-(3-aminocarboxypropyl)-uridine showing the most significant differences. 1-ribosylimidazole-4-acetic acid, a histamine metabolite, was solely found in the supernatants of MCF-10A cells, whereas 1-ribosyl-4-carboxamido-5-aminoimidazole and S-adenosylmethionine occurred only in supernatants of MCF-7 cells.

Conclusion

The obtained results are discussed against the background of pathological changes in cell metabolism, resulting in new perspectives for modified nucleosides and related metabolites as possible biomedical markers for breast carcinoma in vivo.