Cancer Metabolism
Overview
The Sanford Burnham Prebys Cancer Metabolism Core provides a hub within the Institute for analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All of the instruments and approaches are available on a fee-for-service basis to Cancer Center scientists, but also (as capacity permits) to outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.
Services
The Primary Services Offered by the Core are:
- GC/MS or GC/MS/MS-based analysis of metabolites, including:
- Quantification of polar metabolites (such as amino acids, components of glycolysis and TCA pathways) in panels designed for different sample types (cells, medium, tumor/ tissue, serum/ plasma, or “total”) and including 39-89 metabolites.
- Stable isotope (13C, 15N, 2H) tracing of polar metabolites (25 metabolites)
- Fatty acids and cholesterol (quantification and 13C-tracing)
- Short-chain fatty acids (quantification with negative chemical ionization)
- Custom assays of sugars, sugar-phosphates, and related molecules
- Quantification versus standards can be combined with stable isotope tracing. The combination can provide more confidence in identified changes in metabolic activity.
- Measurement of cellular respiration and glycolysis using Seahorse XFp, XFe24 and XFe96 analyzers. These instruments determine rates of extracellular acidification and oxygen consumption by living cells respectively in a 6-well or larger 24 or 96 well formats. From these data, the relative activity of cellular glycolysis versus oxidative phosphorylation, including the balance of ATP production from these two major energetic processes, may be determined.
- Measurement of major substrates and metabolites (glucose, glutamine, lactate, and glutamate) in culture medium using the YSI 2950 analyzer. This instrument is able to rapidly (~1 min per metabolite) determine the concentration of these important metabolism substrates from a small volume of sample (100-200 µL). Using a 96-well format, this analysis provides an economical method to roughly define changes in metabolism (e.g., in proliferating versus quiescent cells), and is also useful for checking that cells in culture have a sufficient supply of the major nutrients glucose and glutamine.
Equipment & Resources
- A Thermo TSQ 9610 gas chromatograph- triple quad mass spectrometer (GC-MS/MS) is used for quantitative analysis of up to 90 polar metabolites from samples including cells, tumors or serum. It is also used for quantification of fatty acids and short-chain fatty acids (SCFA). SCFA are analyzed with negative chemical ionization, which reduces background and allows for low detection limits.
- A Shimadzu QP2010 GC-MS is used for metabolic analyses which include determination of stable isotope (13C, 15N) labeling rates of intra- and extracellular metabolites. 13C labeling can be measured in amino acids, keto and fatty acids, sugars, and sugar phosphates.
- The YSI 2950 metabolite analyzer is able to measure glucose, glutamine, lactate and glutamate in media in 2-3 minutes for all 4 metabolites in a 96-well format. The minimum volume needed is 100 μl. A full 96-well plate may be analyzed in 3-4 hours and results are typically returned the same or next day.
- The XFp Analyzer can measure respiration in most cell types, including primary cells, adherent cells, and suspension cells (with attachment). With a 6 well format, the XFp Miniplate is ideal for pairwise comparisons (in triplicate) and the analysis of precious samples, such as patient-derived and other rare samples. We mainly focus on the Cell Mito Stress Test to measure the key parameters of mitochondrial function: basal respiration, ATP production, proton leak, maximal respiration, and spare respiratory capacity. Other protocols to measure the use of alternate substrates or to calculate the relative production of ATP from glycolysis or oxidative phosphorylation are available.
- The XFe24 Analyzer is similar to the XFp, but well sizes are 2.5x larger and up to 22 samples can be run on one plate. We have available islet capture plates.
- The XFe96 analyzer has the same well size as the XFp and can run up to 92 samples on one plate.
Price List
For a complete list of services, please call (858) 646-1000 ext. 3941 or email us.
| Cancer Metabolism Services | Internal (Subsidized) | Non-Profit | For Profit | Minimum sample number | Code |
|---|---|---|---|---|---|
| GCMS metabolite quantification and stable isotope (13C) tracing (per sample) | |||||
| Polar metabolite GCMS quantification (cells or medium ~40 metabolites) | $40 | $54 | $105.20 | 12 | CMR162 |
| Polar metabolite GCMS quantification (serum or tissue ~55 metabolites) | $44 | $59.40 | $115.72 | 12 | CMR182 |
| Polar metabolite GCMS quantification (total panel ~85 metabolites OR custom assays) | $50 | $67.50 | $131.50 | 12 | CMR183 |
| Polar metabolite 13C GCMS analysis | $59.40 | $44 | $115.72 | 6 | CMR163 |
| Combined GCMS 13C & quant polar metabolites | $78 | $105.30 | $205.14 | 8 | CMR170 |
| Fatty acid & cholesterol GCMS analysis (quantification) | $48 | $64.80 | $126.24 | 12 | CMR164 |
| Fatty acid 13C GCMS analysis | $52 | $70.20 | $126.24 | 6 | CMR171 |
| Combined GCMS 13C & quant fatty acids | $90 | $121.50 | $236.70 | 8 | CMR184 |
| Short-chain fatty acid GCMS quantification | $50 | $67.50 | $131.50 | 12 | CMR172 |
| Sample prep for GC-MS (extra to sample analysis fee) | |||||
| Sample prep – cells or medium, or serum/ plasma | $3 | $4.05 | $7.89 | N/A | CMR175 |
| Sample prep – fecal/ cecum; weighed tumor or tissue | $9 | $12.15 | $23.67 | N/A | CMR177 |
| Sample prep – tumor, tissue, not weighed or needs re-weighing | $15 | $20.25 | $39.45 | N/A | CMR176 |
| Sample prep – urine with urease treatment | $5 | $6.75 | $13.15 | N/A | CMR174 |
| Charges for Seahorse analyzers and YSI Bioanalyzer | |||||
| Seahorse XFp (per plate) (training/ full service) | $200 | $270 | $526 | N/A | CMR166 |
| YSeahorse XFp (per plate) (self-service) | $80 | $108 | $210.40 | N/A | CMR168 |
| Seahorse XFe24 (per plate) (training/ full service) | $300 | $405 | $789 | N/A | CMR178 |
| Seahorse XFe24 (per plate) (self- service) | $190 | $256.50 | $499.70 | N/A | CMR179 |
| Seahorse XFe96 (per plate) (training/ full service) | $450 | $606.50 | $1,183.50 | N/A | CMR180 |
| Seahorse XFe96 (per plate) (self- service) | $190 | $256.50 | $499.70 | N/A | CMR181 |
| YSI metabolite analysis (per plate) | $99 | $133.65 | $260.37 | N/A | CMR167 |
Notes
Sample prep charges (CMR174-177) are for sample extraction for GCMS, and are in addition to the GCMS charges. If samples are submitted as dried extracts the prep charges will not apply. See core for details.
25% discount for samples for GCMS in excess of 30 in a singly batch, rounded to nearest sample (e.g., 32-35 samples, discount of 1 sample).
Self-service rate for Seahorse analyzers includes the cost of plates, XF-medium and reagents.
Contact
David Scott, PhD
David Scott focuses on the development and application of methods for metabolomics, enhanced by the use of stable isotope substrates. Stable isotopes (mainly 13C) provide an added layer of information to metabolomic studies – not only is static pool information obtained, but it is also possible to infer the origins of metabolites and to track flux through metabolic pathways. Methods used include the analysis of small polar metabolites (mainly amino acids and carboxylic acids) and fatty acids by gas chromatography-mass spectrometry. Other techniques are being developed to analyze and quantify an expanded range of (labeled) metabolites. We have applied these methods in a study of the central carbon metabolism in Escherichia coli, and, in several papers, on melanoma metabolism. Investigations of melanoma cells showed the importance of glutamine metabolism under hypoxia, identified a novel route for the utilization of the carbon backbone of glutamine for fatty acid synthesis, and defined pathways for proline synthesis. Other recent work uses alternately labeled sugars to simultaneously track different inputs to glycans in normal cells and cell lines from patients with glycosylation defects.
Please call (858) 646-3100 ext. 3941 or use the button below to send us an email.