Summary of Study ST003664

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 PR002273. The data can be accessed directly via it's Project DOI: 10.21228/M8TC2W 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003664
Study TitleTumour interstitial fluid-enriched phosphoethanolamine suppresses T cell function.
Study SummaryNutrient stress represents a significant barrier for antitumor immunity, and tumor interstitial fluid (TIF) often contains metabolites that hinder immune function. However, it is difficult to isolate the effects of tumor nutrient stress from other suppressive factors. Thus, we employed a chemically-defined cell culture medium based on the metabolomic profile of TIF: Tumor Interstitial Fluid Medium (TIFM). Culture of CD8+ T cells in TIFM limited cell expansion and impaired CD8+ T cell effector functions upon restimulation, suggesting tumor nutrient stress alone is sufficient to drive T cell dysfunction. We identified phosphoethanolamine (pEtn), a phospholipid intermediate, as a driver of T cell dysfunction. pEtn dampened T Cell Receptor (TCR) signaling by depleting T cells of diacylglycerol required for TCR signal transduction. Reduction of pEtn accumulation in tumors improved intratumoral T cell function and tumor control, suggesting pEtn accumulation plays a dominant role in TME immunosuppression.
Institute
University of Chicago
DepartmentComprehensive Cancer Center
LaboratoryMetabolomics Platform
Last NameShah
First NameHardik
Address900 E 57th street, Chicago, IL, 60637, USA
Emailhardikshah@uchicago.edu
Phone7738348830
Submit Date2025-01-14
Num Groups9
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-01-20
Release Version1
Hardik Shah Hardik Shah
https://dx.doi.org/10.21228/M8TC2W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002273
Project DOI:doi: 10.21228/M8TC2W
Project Title:Tumour interstitial fluid-enriched phosphoethanolamine suppresses T cell function
Project Summary:Nutrient stress represents a significant barrier for antitumor immunity, and tumor interstitial fluid (TIF) often contains metabolites that hinder immune function. However, it is difficult to isolate the effects of tumor nutrient stress from other suppressive factors. Thus, we employed a chemically-defined cell culture medium based on the metabolomic profile of TIF: Tumor Interstitial Fluid Medium (TIFM). Culture of CD8+ T cells in TIFM limited cell expansion and impaired CD8+ T cell effector functions upon restimulation, suggesting tumor nutrient stress alone is sufficient to drive T cell dysfunction. We identified phosphoethanolamine (pEtn), a phospholipid intermediate, as a driver of T cell dysfunction. pEtn dampened T Cell Receptor (TCR) signaling by depleting T cells of diacylglycerol required for TCR signal transduction. Reduction of pEtn accumulation in tumors improved intratumoral T cell function and tumor control, suggesting pEtn accumulation plays a dominant role in TME immunosuppression.
Institute:University of Chicago
Department:Comprehensive Cancer Center
Laboratory:UCCC-Metabolomics Platform
Last Name:Shah
First Name:Hardik
Address:900 E 57th street, Chicago, IL, 60637, USA
Email:hardikshah@uchicago.edu
Phone:7738348830

Subject:

Subject ID:SU003796
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Genotype
SA401185Pos_C_D1_35C_D1
SA401186Pos_C_D1_31C_D1
SA401187Pos_C_D1_32C_D1
SA401188Pos_C_D1_34C_D1
SA401189C_D1_31C_D1
SA401190C_D1_32C_D1
SA401191C_D1_34C_D1
SA401192C_D1_35C_D1
SA401193C_D1_36C_D1
SA401194Pos_C_D1_36C_D1
SA401195Pos_C_D3_34C_D3
SA401196Pos_C_D3_32C_D3
SA401197Pos_C_D3_31C_D3
SA401198C_D3_31C_D3
SA401199C_D3_36C_D3
SA401200C_D3_35C_D3
SA401201C_D3_34C_D3
SA401202C_D3_32C_D3
SA401203Pos_C_D3_36C_D3
SA401204Pos_C_D3_35C_D3
SA401205C_D5_35C_D5
SA401206Pos_C_D5_31C_D5
SA401207Pos_C_D5_32C_D5
SA401208C_D5_36C_D5
SA401209C_D5_34C_D5
SA401210C_D5_32C_D5
SA401211C_D5_31C_D5
SA401212Pos_C_D5_34C_D5
SA401213Pos_C_D5_35C_D5
SA401214Pos_C_D5_36C_D5
SA401215Ctrl_32Ctrl
SA401216Pos_Ctrl_36Ctrl
SA401217Pos_Ctrl_35Ctrl
SA401218Pos_Ctrl_34Ctrl
SA401219Pos_Ctrl_32Ctrl
SA401220Ctrl_31Ctrl
SA401221Pos_Ctrl_31Ctrl
SA401222Ctrl_36Ctrl
SA401223Ctrl_35Ctrl
SA401224Ctrl_34Ctrl
SA401225Pos_PC_D1_32PC_D1
SA401226Pos_PC_D1_36PC_D1
SA401227Pos_PC_D1_35PC_D1
SA401228Pos_PC_D1_34PC_D1
SA401229Pos_PC_D1_31PC_D1
SA401230PC_D1_31PC_D1
SA401231PC_D1_32PC_D1
SA401232PC_D1_34PC_D1
SA401233PC_D1_35PC_D1
SA401234PC_D1_36PC_D1
SA401235PC_D3_34PC_D3
SA401236Pos_PC_D3_34PC_D3
SA401237Pos_PC_D3_35PC_D3
SA401238Pos_PC_D3_36PC_D3
SA401239PC_D3_31PC_D3
SA401240PC_D3_32PC_D3
SA401241PC_D3_35PC_D3
SA401242Pos_PC_D3_32PC_D3
SA401243PC_D3_36PC_D3
SA401244Pos_PC_D3_31PC_D3
SA401245PC_D5_32PC_D5
SA401246PC_D5_34PC_D5
SA401247PC_D5_35PC_D5
SA401248PC_D5_36PC_D5
SA401249Pos_PC_D5_32PC_D5
SA401250Pos_PC_D5_34PC_D5
SA401251PC_D5_31PC_D5
SA401252Pos_PC_D5_35PC_D5
SA401253Pos_PC_D5_36PC_D5
SA401254Pos_PC_D5_31PC_D5
SA401255Pos_PE_D1_31PE_D1
SA401256Pos_PE_D1_32PE_D1
SA401257Pos_PE_D1_34PE_D1
SA401258Pos_PE_D1_35PE_D1
SA401259Pos_PE_D1_36PE_D1
SA401260PE_D1_34PE_D1
SA401261PE_D1_35PE_D1
SA401262PE_D1_36PE_D1
SA401263PE_D1_31PE_D1
SA401264PE_D1_32PE_D1
SA401265PE_D3_34PE_D3
SA401266Pos_PE_D3_36PE_D3
SA401267Pos_PE_D3_35PE_D3
SA401268Pos_PE_D3_34PE_D3
SA401269Pos_PE_D3_32PE_D3
SA401270Pos_PE_D3_31PE_D3
SA401271PE_D3_35PE_D3
SA401272PE_D3_31PE_D3
SA401273PE_D3_36PE_D3
SA401274PE_D3_32PE_D3
SA401275PE_D5_31PE_D5
SA401276PE_D5_32PE_D5
SA401277PE_D5_34PE_D5
SA401278PE_D5_35PE_D5
SA401279PE_D5_36PE_D5
SA401280Pos_PE_D5_31PE_D5
SA401281Pos_PE_D5_32PE_D5
SA401282Pos_PE_D5_34PE_D5
SA401283Pos_PE_D5_35PE_D5
SA401284Pos_PE_D5_36PE_D5
Showing results 1 to 100 of 100

Collection:

Collection ID:CO003789
Collection Summary:Single cell suspensions of OT-I splenocytes were cultured with SIINFEKL peptide and 50U/mL of IL-2 in RPMI for 24 hours. After the initial 24 hours of activation, cells were cultured in RPMI with 50U/mL of IL-2 until they were transferred into RPMI.
Sample Type:T-cells

Treatment:

Treatment ID:TR003805
Treatment Summary:RPMI was supplemented with pEtn, choline or pCholine to match metabolite concentrations in TIFM for 1, 3 or 5 days prior to analysis on day 7 after initial activation. After treatment, 2 x 106 cells were pelleted and flash frozen.

Sample Preparation:

Sampleprep ID:SP003803
Sampleprep Summary:For lipidomic analysis, 20uL of Avanti SPLASH deuterated internal standard mix (1:100 dilution) was added to frozen cell pellets, followed by extraction with a modified 44 method. In brief, ice-cold methanol containing 0.1mg/mL butylated hydroxytoluene was added to the cell pellet followed by sonication for 3 minutes and shaking for 5 mins at 15°C and 1000 rpm using Thermomixer. Then 900 uL of methyl-tert-butyl ether (MTBE) was added to the cell pellets tubes to extract the lipid species. The tubes were vortexed for 15 mins at 4°C and 1000 rpm on a Thermomixer. The phase separation was induced by adding 300 µL of ice-cold water followed by sonication for 3 mins, vortex for 15 mins at 15°C and 1000 rpm, and centrifuge at 21,000g and 4°C for 15 mins. The upper organic layer (400µL) was dried using the Genevac EZ-2.4 elite evaporator and stored at -80°C. One aliquot was reserved for the positive ionization mode and the second aliquot for the negative ionization mode. On the day of analysis, the dried lipid extract was re-suspended in 40µL of 3/2/1 isopropanol/acetonitrile/water at room temperature, sonicated for 3 minutes, vortex for 15 mins at 15°C and 2000 rpm, and 25µL of supernatant was transferred to LC-MS vial. A pooled QC sample was generated using the remaining samples.

Chromatography:

Chromatography ID:CH004574
Chromatography Summary:Lipids were separated on Thermo Scientific Accucore C30 (2.1x150 mm, 2.6µm) column connected to a Vanquish Horizon UHPLC system and IQ-X tribrid mass spectrometers. The column temperature, injection volume, and flow rate were 45°C, 4 µL, and 0.26 mL/min, respectively. The mobile phase A (MPA) was 60/40 acetonitrile/water, 10mM ammonium formate + 0.1% formic acid and MPB was 89.1/9.9/0.99 isopropanol/acetonitrile/water, 10 mM ammonium formate + 0.1% formic acid. The chromatographic gradient was 0 minute: 30%B, 2.00 minutes (mins): 43% B, 2.1 mins: 55%B, 12.00 mins: 65%B, 18.00 mins: 85%B, 20.00 mins: 100%B, 25.00 mins:100%B, 25.1 mins:30%B and 30.00 mins:30%B.
Instrument Name:Thermo Scientific Vanquish Horizon UHPLC
Column Name:Thermo Scientific Accucore C30 (150 x 2.1 mm, 2.6 µm)
Column Temperature:45℃
Flow Gradient:0 minute: 30%B, 2.00 minutes (mins): 43% B, 2.1 mins: 55%B, 12.00 mins: 65%B, 18.00 mins: 85%B, 20.00 mins: 100%B, 25.00 mins:100%B, 25.1 mins:30%B and 30.00 mins:30%B.
Flow Rate:0.260 mL/min
Injection Temperature:15℃
Solvent A:60% Acetonitrile/40% Water; 10mM ammonium formate; 0.1% formic acid
Solvent B:89.1% isopropanol/9.9% acetonitrile/0.99% water; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006020
Analysis Type:MS
Chromatography ID:CH004574
Num Factors:10
Num Metabolites:444
Rt Units:Minutes
Units:A.U.
  
Analysis ID:AN006021
Analysis Type:MS
Chromatography ID:CH004574
Num Factors:10
Num Metabolites:65
Rt Units:Minutes
Units:A.U.
  logo