Fast Filtration of Bacterial or Mammalian Suspension Cell Cultures for Optimal Metabolomics Results

The metabolome offers real time detection of the adaptive, multi-parametric response of the organisms to environmental changes, pathophysiological stimuli or genetic modifications and thus rationalizes the optimization of cell cultures in bioprocessing. In bioprocessing the measurement of physiological intracellular metabolite levels is imperative for successful applications. However, a sampling method applicable to all cell types with little to no validation effort which simultaneously offers high recovery rates, high metabolite coverage and sufficient removal of extracellular contaminations is still missing. Here, quenching, centrifugation and fast filtration were compared and fast filtration in combination with a stabilizing washing solution was identified as the most promising sampling method. Different influencing factors such as filter type, vacuum pressure, washing solutions were comprehensively tested. The improved fast filtration method (MxP^® FastQuench) followed by routine lipid/polar extraction delivers a broad metabolite coverage and recovery reflecting well physiological intracellular metabolite levels for different cell types, such as bacteria (Escherichia coli) as well as mammalian cells chinese hamster ovary (CHO) and mouse myeloma cells (NS0).The proposed MxP^® FastQuench allows sampling, i.e. separation of cells from medium with washing and quenching, in less than 30 seconds and is robustly designed to be applicable to all cell types. The washing solution contains the carbon source respectively the ¹³C-labeled carbon source to avoid nutritional stress during sampling. This method is also compatible with automation which would further reduce sampling times and the variability of metabolite profiling data.

Characterization and comparison of toxin-producing isolates of Dinophysis acuminata from New England and Canada

Following the identification of the first toxic isolate of Dinophysis acuminata from the northwestern Atlantic, we conducted detailed investigations into the morphology, phylogeny, physiology, and toxigenicity of three isolates from three sites within the northeastern U.S./Canada region: Eel Pond and Martha's Vineyard, Massachusetts, and the Bay of Fundy. Another isolate, collected from the Gulf of Mexico, was grown under the same light, temperature, and prey conditions for comparison. Despite observed phenotypic heterogeneity, morphometrics and molecular evidence classified the three northwestern Atlantic isolates as D. acuminata Claparède & Lachmann, whereas the isolate from the Gulf of Mexico was morphologically identified as D. cf. ovum. Physiological and toxin analyses supported these classifications, with the three northwestern Atlantic isolates being more similar to each other with respect to growth rate, toxin profile, and diarrhetic shellfish poisoning (DSP) toxin content (okadaic acid + dinophysistoxin 1/cell) than they were to the isolate from the Gulf of Mexico, which had toxin profiles similar to those published for D. cf. ovum F. Schütt. The DSP toxin content, 0.01-1.8 pg okadaic acid (OA) + dinophysistoxin (DTX1) per cell, of the three northwestern Atlantic isolates was low relative to other D. acuminata strains from elsewhere in the world, consistent with the relative scarcity of shellfish harvesting closures due to DSP toxins in the northeastern U.S. and Canada. If this pattern is repeated with the analyses of more geographically and temporally dispersed isolates from the region, it would appear that the risk of significant DSP toxin outbreaks in the northwestern Atlantic is low to moderate. Finally, the morphological, physiological, and toxicological variability within D. acuminata may reflect spatial (and/or temporal) population structure, and suggests that sub-specific resolution may be helpful in characterizing bloom dynamics and predicting toxicity.

Abstract 1895: The influence of gemcitabine and its metabolites on cancer cell metabolism

The nucleoside analogue gemcitabine is marketed for patients with locally advanced or metastatic adenocarcinoma of the pancreas as single agent and first-line treatment. In addition, it is widely used for the treatment of various carcinomas and approved by the FDA for several combination treatments. However, many patients develop gemcitabine-resistant tumor cells. This phenomenon is of special concern in pancreatic cancers, as these tumors are known to harbor more than 60 different mutations. In addition, gemcitabine is rapidly metabolized upon entry into the cells, leading to the development of drug metabolites (mono-, di-, tri-phosphates, deaminated and subsequently phosphorylated metabolites, etc.) with minimal differences in molecular mass and partly hydrophilic properties. As a result, quantitative analysis - a prerequisite for understanding the metabolism and the mechanism of action - is extremely difficult. This poses enormous challenges for overcoming gemcitabine resistance and for the development of novel active pharmaceutical ingredients addressing other, additional targets in pancreatic and other cancers. Therefore, pharmaceutical companies need more accurate data on how is gemcitabine metabolized, whether various subpopulations of patients react differently to the drug and on which biomarkers associated with drug sensitivity and/or resistances exist.

Here, we report a new LC-MS/MS method development at Metanomics Health that allows for the first time to accurately assess and quantify the entire range of gemcitabine metabolites. The new method works in high-throughput mode analyzing samples from full blood as well as various cells and tissue in respect to their response to gemcitabine and its derivatives. The analytical platform also includes about 90 key energy metabolites from glycolysis and TCA pathways, nucleobases, amino acids, co-enzymes, etc. This comprehensive analysis covering the key metabolites involved in cancer metabolism can be performed from a single sample in one run and in high-throughput mode.

The detection and in-depth analysis of gemcitabine and its metabolites therefore provides an invaluable basis for a better understanding of gemcitabine's self-potentiation mechanisms, its mechanisms of action, as well as mechanisms that lead to the inactivation of gemcitabine or to gemcitabine-mediated activation of treatment resistance. Subsequently, this might support the development of new combination therapies. To determine remaining gemcitabine activity in patients in the long run, metabolite profiling seems a sagacious next step. This approach may support the decision for the appropriate timing of the next treatment dose, which likely contributes to saving costs, reducing side-effects and even slowing down the process of gemcitabine resistance development.

Citation Format: Elie Fux, Hajo Schiewe, Niels Moeller, Regina Reszka, Patricia Ruiz Nopinger. The influence of gemcitabine and its metabolites on cancer cell metabolism. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1895. doi:10.1158/1538-7445.AM2013-1895

Development of an ultra-performance liquid chromatography–mass spectrometry method for the detection of lipophilic marine toxins

A rapid method for the detection of marine toxins was developed using an ultra-performance liquid chromatography (UPLC) system coupled to a latest generation mass spectrometry (MS) system. The analysis of 21 lipophilic marine toxins was achieved on an Acquity C18 column using a water-acetonitrile gradient with a cycle time of 6.6 min, reducing analysis time by more than a factor two compared to HPLC while maintaining peak resolution. Linear ranges, limits of detection and limits of quantification were established for okadaic acid (OA), pectenotoxin-2, azaspiracid-1 (AZA1), yessotoxin, gymnodimine and 13-desmethylspirolide C. The method was found to be accurate when using a triplicate methanolic extraction. Matrix effects were assessed by standard addition of OA and AZA1 in extracts of raw and heat-treated flesh of mussels and oysters. For the analysis of AZA1, the UPLC-MS method was always prone to signal suppression, while for OA analysis signal suppression was observed in extracts of raw shellfish flesh and signal enhancement in extracts of heat-treated flesh. Matrix effects occurring in the method presented are diminished compared to previous studies.

Unmixing coral fluorescence emission spectra and predicting new spectra under different excitation conditions

An algorithm was developed that uses prototype spectra and least-squares minimization to unmix the relative contributions of individual pigments to the composite fluorescence emission spectrum of reef corals. Field measurements indicated that it was necessary to include allowance for spectral shift of the wavelength peak of the prototype emission spectra. The unmixed spectra are used to predict the shape and amplitude of composite spectra that would be expected under different excitation conditions. We found that, for cases in which the pigments occur singly or with significant spectral separation, it is necessary to consider the properties of the excitation light sources, only, to make accurate predictions. In cases with spectral overlap the contribution of interpigment coupling cannot be neglected.