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Unraveling altered RNA metabolism in pancreatic cancer cells by liquid-chromatography coupling to ion mobility mass spectrometry

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Abstract

Ion mobility coupling to mass spectrometry facilitates enhanced identification certitude. Further coupling to liquid chromatography results in multi-dimensional analytical methods, especially suitable for complex matrices with structurally similar compounds. Modified nucleosides represent a large group of very similar members linked to aberrant proliferation. Besides basal production under physiological conditions, they are increasingly excreted by transformed cells and subsequently discussed as putative biomarkers for various cancer types. Here, we report a method for modified nucleosides covering 37 species. We determined collisional cross-sections with high reproducibility from pure analytical standards. For sample purification, we applied an optimized phenylboronic acid solid-phase extraction on media obtained from four different pancreatic cancer cell lines. Our analysis could discriminate different subtypes of pancreatic cancer cell lines. Importantly, they could clearly be separated from a pancreatic control cell line as well as blank medium. m1A, m27G, and Asm were the most important features discriminating cancer cell lines derived from well-differentiated and poorly differentiated cancers. Eventually, we suggest the analytical method reported here for future tumor-marker identification studies.

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Acknowledgements

This work was supported by Project B01 of the collaborative research initiative (SFB 1140 - KIDGEM) to M.S. and B.K. by the German Research Foundation (DFG).

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Author notes

  1. Simon Lagies and Manuel Schlimpert contributed equally to this work.

Authors and Affiliations

  1. Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany

    Simon Lagies, Manuel Schlimpert, Lukas M. Braun, Michel Kather, Johannes Plagge & Bernd Kammerer

  2. Institute of Biology II, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany

    Simon Lagies & Manuel Schlimpert

  3. Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, Albertstr. 19A, 79104, Freiburg, Germany

    Simon Lagies & Manuel Schlimpert

  4. Department of General- and Visceral Surgery, University of Freiburg Medical Center, Hugstetter Str. 55, 79106, Freiburg, Germany

    Lukas M. Braun & Uwe A. Wittel

  5. Faculty of Chemistry and Pharmacy, Albert-Ludwigs-University Freiburg, Hebelstr. 27, 79104, Freiburg, Germany

    Michel Kather

  6. Hermann Staudinger Graduate School, University of Freiburg, Hebelstr. 27, 79104, Freiburg, Germany

    Michel Kather

  7. Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany

    Thalia Erbes

  8. BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 16, 79104, Freiburg, Germany

    Bernd Kammerer

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  1. Simon Lagies
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Contributions

Simon Lagies, Manuel Schlimpert, Lukas M. Braun, Thalia Erbes, Uwe A. Wittel, and Bernd Kammerer designed the study. Simon Lagies, Manuel Schlimpert, Lukas M. Braun, and Michel Kather performed the experiments and data analysis. Johannes Plagge aided in data processing and image creation. Simon Lagies, Lukas M. Braun, and Manuel Schlimpert wrote the manuscript.

Corresponding author

Correspondence to Bernd Kammerer.

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Informed consent was obtained for KHM1106 cell line usage and approved by the local Ethics Committee Freiburg (126/17 and 371/14) and registered at the German Clinical Trials Register (DRKS-ID DRKS00007561).

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The authors declare that they have no conflict of interest.

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Published in the topical collection Close-Up of Current Developments in Ion Mobility Spectrometry with guest editor Gérard Hopfgartner.

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Lagies, S., Schlimpert, M., Braun, L.M. et al. Unraveling altered RNA metabolism in pancreatic cancer cells by liquid-chromatography coupling to ion mobility mass spectrometry. Anal Bioanal Chem 411, 6319–6328 (2019). https://doi.org/10.1007/s00216-019-01814-1

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