Summary of Study ST002534

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 PR001630. The data can be accessed directly via it's Project DOI: 10.21228/M80T52 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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.

Study ID	ST002534
Study Title	Using Mass Spectrometry Imaging to Map Fluxes Quantitatively in the Tumor Ecosystem
Study Summary	Tumors are comprised of a multitude of cell types spanning different microenvironments. Mass spectrometry imaging (MSI) has the potential to identify metabolic patterns within the tumor ecosystem and surrounding tissues, but conventional workflows have not yet fully integrated the breadth of experimental techniques in metabolomics. Here, we combine MSI, stable isotope labeling, and a spatial variant of Isotopologue Spectral Analysis to map distributions of metabolite abundances, nutrient contributions, and metabolic turnover fluxes across the brains of mice harboring GL261 glioma, a widely used model for glioblastoma. When integrated with MSI, the combination of ion mobility, Desorption Electrospray Ionization, and Matrix Assisted Laser Desorption revealed disruption in multiple anabolic pathways. De novo fatty acid synthesis flux was determined to be increased by approximately 3-fold in glioma relative to surrounding healthy tissue. Fatty acid elongation flux was elevated even higher at 8-fold and highlights the importance of elongase activity in glioma. The fluxes we examined were uniformly increased throughout the entire tumor region, revealing a high degree of metabolic homogeneity in our model of glioblastoma.
Institute	Washington University in St. Louis
Department	Chemistry
Laboratory	Patti
Last Name	Stancliffe
First Name	Ethan
Address	1 Brookings Dr. Campus Box 1134, St. Louis, MO 63105
Email	estancliffe@wustl.edu
Phone	3194644881
Submit Date	2023-03-24
Num Groups	2
Total Subjects	8
Num Females	8
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2023-04-13
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001630
Project DOI:	doi: 10.21228/M80T52
Project Title:	Using Mass Spectrometry Imaging to Map Fluxes Quantitatively in the Tumor Ecosystem
Project Summary:	Tumors are comprised of a multitude of cell types spanning different microenvironments. Mass spectrometry imaging (MSI) has the potential to identify metabolic patterns within the tumor ecosystem and surrounding tissues, but conventional workflows have not yet fully integrated the breadth of experimental techniques in metabolomics. Here, we combine MSI, stable isotope labeling, and a spatial variant of Isotopologue Spectral Analysis to map distributions of metabolite abundances, nutrient contributions, and metabolic turnover fluxes across the brains of mice harboring GL261 glioma, a widely used model for glioblastoma. When integrated with MSI, the combination of ion mobility, Desorption Electrospray Ionization, and Matrix Assisted Laser Desorption revealed disruption in multiple anabolic pathways. De novo fatty acid synthesis flux was determined to be increased by approximately 3-fold in glioma relative to surrounding healthy tissue. Fatty acid elongation flux was elevated even higher at 8-fold and highlights the importance of elongase activity in glioma. The fluxes we examined were uniformly increased throughout the entire tumor region, revealing a high degree of metabolic homogeneity in our model of glioblastoma.
Institute:	Washington University in St. Louis
Last Name:	Stancliffe
First Name:	Ethan
Address:	1 Brookings Dr. Campus Box 1134, St. Louis, MO 63105
Email:	estancliffe@wustl.edu
Phone:	3194644881

Subject:

Subject ID:	SU002634
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample type	Isotopically labeled	Group
SA254925	1-3_nontumor	brain tissue	no	brain_nontumor
SA254926	1-5_nontumor	brain tissue	no	brain_nontumor
SA254927	2-5_nontumor	brain tissue	no	brain_nontumor
SA254928	1-1_nontumor	brain tissue	no	brain_nontumor
SA254929	2-3_nontumor	brain tissue	no	brain_nontumor
SA254930	1-3_tumor	brain tissue	no	brain_tumor
SA254931	2-5_tumor	brain tissue	no	brain_tumor
SA254932	2-3_tumor	brain tissue	no	brain_tumor
SA254933	1-1_tumor	brain tissue	no	brain_tumor
SA254934	1-5_tumor	brain tissue	no	brain_tumor
SA254935	4-1_nontumor	brain tissue	yes	brain_nontumor
SA254936	4-2_nontumor	brain tissue	yes	brain_nontumor
SA254937	4-3_nontumor	brain tissue	yes	brain_nontumor
SA254938	4-4_nontumor	brain tissue	yes	brain_nontumor
SA254939	4-3_tumor	brain tissue	yes	brain_tumor
SA254940	4-4_tumor	brain tissue	yes	brain_tumor
SA254941	4-1_tumor	brain tissue	yes	brain_tumor
SA254942	4-2_tumor	brain tissue	yes	brain_tumor
SA254943	4-2_serum	serum	yes	serum
SA254944	4-4_serum	serum	yes	serum
SA254945	4-1_serum	serum	yes	serum
SA254946	4-3_serum	serum	yes	serum

Showing results 1 to 22 of 22

Showing results 1 to 22 of 22

Collection:

Collection ID:	CO002627
Collection Summary:	Brains were embedded in 5% wt. carboxymethyl cellulose (Millipore Sigma) in water and stored at -80 °C. Next, 20 µm thick sections were collected at -20 °C by using a CM1860 cryostat (Leica Biosystems). Superfrost Plus slides (Thermo Fisher Scientific) were used after cleaning with ethanol. Sections were dried under vacuum, stored at -80 °C until use, and thawed under vacuum immediately prior to analysis. For MALDI, 10 µm thick sections were collected on SiO2 passivated, indium tin oxide coated polished float glass slides (Delta Technologies Limited, Loveland, CO, USA). Serial 50 µm thick sections were collected for extraction and LC/MS analysis after dividing between tumor-containing and non-tumor hemispheres (as described below).
Sample Type:	Brain

Treatment:

Treatment ID:	TR002646
Treatment Summary:	No treatments were applied.

Sample Preparation:

Sampleprep ID:	SP002640
Sampleprep Summary:	Sections of 50 µm brain tissue were cut into left (tumor) and right (non-tumor) hemispheres with a razor blade and collected into Eppendorf tubes while being kept frozen in the cryostat. The samples were then extracted with 2:2:1 acetonitrile, methanol, water at a ratio of 80 µL per mg wet weight. The weight was calculated based on area and thickness of the sections. The solvent was added to the tissue and vigorously vortexed. For serum analysis, 5 µL serum was mixed with 45 µL of a 4:4:1 mixture of acetonitrile, methanol, water and vortexed. Extraction blanks were prepared with 5 µL water instead of serum. All samples were kept at -20 °C overnight. After centrifugation at 14,000 g for 10 min at 4 °C, the supernatant was transferred to an LC/MS vial.

Sampleprep ID:

SP002640

Sampleprep Summary:

Sections of 50 µm brain tissue were cut into left (tumor) and right (non-tumor) hemispheres with a razor blade and collected into Eppendorf tubes while being kept frozen in the cryostat. The samples were then extracted with 2:2:1 acetonitrile, methanol, water at a ratio of 80 µL per mg wet weight. The weight was calculated based on area and thickness of the sections. The solvent was added to the tissue and vigorously vortexed. For serum analysis, 5 µL serum was mixed with 45 µL of a 4:4:1 mixture of acetonitrile, methanol, water and vortexed. Extraction blanks were prepared with 5 µL water instead of serum. All samples were kept at -20 °C overnight. After centrifugation at 14,000 g for 10 min at 4 °C, the supernatant was transferred to an LC/MS vial.

Combined analysis:

Analysis ID	AN004169
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Vanquish
Column	SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Orbitrap ID-X tribrid
Ion Mode	UNSPECIFIED
Units	Peak areas

Chromatography:

Chromatography ID:	CH003087
Chromatography Summary:	Metabolites were separated via hydrophilic interaction liquid chromatography (HILIC) by using a SeQuant ZIC-pHILIC column (100 x 2.1 mm, 5 µm, polymer, Merck-Millipore) with a ZIC-pHILIC guard column (20 mm x 2.1 mm, 5 µm). The column compartment temperature was 40 °C and the flow rate was set to 250 µL min-1. The mobile phases consisted of A: 95% water, 5% acetonitrile, 20 mM ammonium bicarbonate, 0.1% ammonium hydroxide solution (25% ammonia in water), 5 µM medronic acid; and B: 95% acetonitrile, 5% water. The following linear gradient was applied: 0 to 1 min, 90% B; 12 min, 35% B; 12.5 to 14.5 min, 25% B; 15 min, 90% B followed by a re-equilibration phase of 4 min at 400 µL min-1 and 2 min at 250 µL min-1. The samples were kept at 6 °C in the autosampler. The injection volume was 5 µL.
Instrument Name:	Thermo Vanquish
Column Name:	SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Temperature:	40 °C
Flow Gradient:	0 to 1 min, 90% B; 12 min, 35% B; 12.5 to 14.5 min, 25% B; 15 min, 90% B followed by a re-equilibration phase of 4 min at 400 µL min-1 and 2 min at 250 µL min-1
Flow Rate:	250 µL min-1
Solvent A:	95% water, 5% acetonitrile, 20 mM ammonium bicarbonate, 0.1% ammonium hydroxide solution (25% ammonia in water), 5 µM medronic acid
Solvent B:	95% acetonitrile, 5% water
Chromatography Type:	HILIC

MS:

MS ID:	MS003916
Analysis ID:	AN004169
Instrument Name:	Thermo Orbitrap ID-X tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	A Vanquish UHPLC system was coupled to an Orbitrap ID-X Tribrid mass spectrometer (Thermo Fisher Scientific) via electrospray ionization with the following source conditions: sheath gas flow 50 arbitrary units (Arb), auxiliary gas flow 10 Arb, sweep gas flow 1 Arb, ion transfer tube temperature 300 °C, vaporizer temperature 200 °C respectively. The RF lens value was 60%. Data were acquired in negative and positive polarity with a spray voltage of 2.8 kV and 3.5 kV, respectively. MS1 data were acquired from 67-900 m/z at a resolution of 120,000 with an automatic gain control (AGC) target of 2e5 and a maximum injection time of 200 ms in polarity switching mode. MS2 data for metabolite identification were acquired at a resolution of 15,000 with an AGC target of 2.5e4 and a maximum injection time of 70 ms in negative and positive mode separately. A 5 ppm mass error and 10 s dynamic exclusion were applied.
Ion Mode:	UNSPECIFIED