Summary of Study ST001119

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000750. The data can be accessed directly via it's Project DOI: 10.21228/M8QX2G This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001119
Study TitleQuantification of microenvironmental metabolites in murine cancers reveals determinants of tumor nutrient availability
Study SummaryCancer cell metabolism is heavily influenced by microenvironmental factors, including nutrient availability. Therefore, knowledge of microenvironmental nutrient levels is essential to understand tumor metabolism. To measure the extracellular nutrient levels available to tumors, we developed a quantitative metabolomics method to measure the absolute concentrations of >118 metabolites in plasma and tumor interstitial fluid, the extracellular fluid that perfuses tumors. Comparison of nutrient levels in tumor interstitial fluid and plasma revealed that the nutrients available to tumors differ from those present in circulation. Further, by comparing interstitial fluid nutrient levels between autochthonous and transplant models of murine pancreatic and lung adenocarcinoma, we found that tumor type, anatomical location and animal diet affect local nutrient availability. These data provide a comprehensive characterization of the nutrients present in the tumor microenvironment of widely used models of lung and pancreatic cancer and identify factors that influence metabolite levels in tumors.
Institute
University of Chicago
Last NameMuir
First NameAlexander
Address929 E 57th St. W GCIS 306, Chicago, Illinois, 60637, USA
Emailmuir.alexander@gmail.com
Phone5104950975
Submit Date2019-01-03
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-03-06
Release Version1
Alexander Muir Alexander Muir
https://dx.doi.org/10.21228/M8QX2G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP001184
Sampleprep Summary:Quantification of metabolite levels in TIF and plasma In order to quantitate metabolites in TIF and plasma samples, we first constructed a library of 149 chemical standards of plasma polar metabolites (see Supplementary File 1 for suppliers for each chemical standard). These compounds were selected to encompass a number of metabolic processes and have previously been included in efforts to profile plasma polar metabolites by LC/MS (Cantor et al., 2017; Evans et al., 2009; Lawton et al., 2008; Mazzone et al., 2016). We pooled these metabolites into 7 separate chemical standard pools (Supplementary File 1). To do this, each metabolite in a given pool was weighed and then mixed (6 cycles of 1 min. mixing at 25 Hz followed by 3 min. resting) using a Mixer Mill MM301 (Retsch, Düsseldorf, Germany), and mixed metabolite powder stocks were stored at -20°C prior to resuspension and analysis. Stock solutions of the mixed standards pools containing ~5mM, ~1mM, ~300µM, ~100µM, ~30µM, ~10µM, ~3µM and ~1µM of each metabolite were made in HPLC grade water and were stored at -80°C (see Supplementary File 1 for the concentration of each metabolite in the external standard pools). We refer to these stock solutions as “external standard pools” throughout. External standard pools were used to confirm the retention time and m/z for each analyte and provide standards to quantitate concentrations of stable isotope labeled internal standards used in downstream analysis, as well as to quantitate metabolite concentrations in TIF and plasma samples directly where internal standards were not available (see below for details). To extract polar metabolites from plasma, TIF or the external standard pools, 5µL of TIF, plasma or external sample pools was mixed with 45uL of acetonitrile:methanol:formic acid (75:25:0.1) extraction buffer including the following isotopically labeled internal standards: 13C labeled yeast extract (Cambridge Isotope Laboratory, Andover, MA, ISO1), 13C3 lactate (Sigma Aldrich, Darmstadt, Germany, 485926), 13C3 glycerol (Cambridge Isotope Laboratory, Andover, MA, CLM-1510), 13C6 15N2 cystine (Cambridge Isotope Laboratory, Andover, MA, CNLM-4244), 2H9 choline (Cambridge Isotope Laboratory, Andover, MA, DLM-549), 13C4 3-hydroxybutyrate (Cambridge Isotope Laboratory, Andover, MA, CLM-3853), 13C6 glucose (Cambridge Isotope Laboratory, Andover, MA, CLM-1396), 13C2 15N taurine (Cambridge Isotope Laboratory, Andover, MA, CNLM-10253), 2H3 creatinine (Cambridge Isotope Laboratory, Andover, MA, DLM-3653), 8-13C adenine (Cambridge Isotope Laboratory, Andover, MA, CLM-1654), 13C5 hypoxanthine (Cambridge Isotope Laboratory, Andover, MA, CLM-8042), 8-13C guanine (Cambridge Isotope Laboratory, Andover, MA, CLM-1019), 13C3 serine (Cambridge Isotope Laboratory, Andover, MA, CLM-1574) and 13C2 glycine (Cambridge Isotope Laboratory, Andover, MA, CLM-1017). All solvents used in the extraction buffer were HPLC grade. Samples were then vortexed for 10 min. at 4°C and insoluble material was sedimented by centrifugation at 15kg for 10 min. at 4°C. 20µL of the soluble polar metabolite extract was taken for LC/MS analysis.
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