Influence of Drying Method on NMR-Based Metabolic Profiling of Human Cell Lines

Irina Petrova; Shenyuan Xu; William C Joesten; Shuisong Ni; Michael A Kennedy

doi:10.3390/metabo9110256

Influence of Drying Method on NMR-Based Metabolic Profiling of Human Cell Lines

Metabolites. 2019 Oct 31;9(11):256. doi: 10.3390/metabo9110256.

Authors

Irina Petrova¹, Shenyuan Xu², William C Joesten³, Shuisong Ni⁴, Michael A Kennedy⁵

Affiliations

¹ Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA. petrovi@miamioh.edu.
² Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA. xus2@miamioh.edu.
³ Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA. joestewc@miamioh.edu.
⁴ Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA. nis@miamioh.edu.
⁵ Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA. kennedm4@miamioh.edu.

Abstract

Metabolic profiling of cell line and tissue extracts involves sample processing that includes a drying step prior to re-dissolving the cell or tissue extracts in a buffer for analysis by GC/LC-MS or NMR. Two of the most commonly used drying techniques are centrifugal evaporation under vacuum (SpeedVac) and lyophilization. Here, NMR spectroscopy was used to determine how the metabolic profiles of hydrophilic extracts of three human pancreatic cancer cell lines, MiaPaCa-2, Panc-1 and AsPC-1, were influenced by the choice of drying technique. In each of the three cell lines, 40-50 metabolites were identified as having statistically significant differences in abundance in redissolved extract samples depending on the drying technique used during sample preparation. In addition to these differences, some metabolites were only present in the lyophilized samples, for example, n-methyl-α-aminoisobutyric acid, n-methylnicotimamide, sarcosine and 3-hydroxyisovaleric acid, whereas some metabolites were only present in SpeedVac dried samples, for example, trimethylamine. This research demonstrates that the choice of drying technique used during the preparation of samples of human cell lines or tissue extracts can significantly influence the observed metabolome, making it important to carefully consider the selection of a drying method prior to preparation of such samples for metabolic profiling.

Keywords: AsPC-1; MiaPaCa-2; NMR; Panc-1; cell line; human cell line; metabolic profiling; metabolomics; metabonomics; nuclear magnetic resonance spectroscopy.