Summary of Study ST004455
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 PR002815. The data can be accessed directly via it's Project DOI: 10.21228/M8SN90 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004455 |
| Study Title | Pyruvate Kinase Muscle (PKM)-2 promotes CD4 T cell survival by regulating pyruvate oxidation during homeostasis and expansion |
| Study Summary | Metabolomics was done on sorted thymic T cell populations. SP4 (CD4+CD8-) cells exhibited the highest relative levels of the pyruvate-derived end product lactate, whereas DN (CD4-CD-) cells showed overall elevated levels of TCA cycle metabolites, indicating a divergence in pyruvate utilization between these subsets. Both SP4 and DN cells also had increased levels of the ancillary metabolites serine and glycine compared to other thymic populations. In contrast, DP (CD4+CD8+) cells, characterized by low PKM2 expression and activity, displayed reduced levels of both glycolytic and TCA intermediates. Interestingly, despite having elevated PKM activity, SP8 (CD4-CD8+) cells mirrored the metabolic profile of DP cells, with similarly diminished glycolytic and TCA metabolite levels. |
| Institute | National Cancer Institute |
| Department | Center for Cancer Research |
| Laboratory | Cancer Innovation Laboratory |
| Last Name | Subleski |
| First Name | Jeff |
| Address | 1050 Boyles Street, Frederick, MD, 21713 |
| subleskj@mail.nih.gov | |
| Phone | 301-846-1515 |
| Submit Date | 2025-11-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2026-01-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002815 |
| Project DOI: | doi: 10.21228/M8SN90 |
| Project Title: | Pyruvate Kinase Muscle (PKM)-2 promotes CD4 T cell survival by regulating pyruvate oxidation during homeostasis and expansion |
| Project Summary: | Metabolomics was done on sorted thymic T cell populations. SP4 (CD4+CD8-) cells exhibited the highest relative levels of the pyruvate-derived end product lactate, whereas DN (CD4-CD-) cells showed overall elevated levels of TCA cycle metabolites, indicating a divergence in pyruvate utilization between these subsets. Both SP4 and DN cells also had increased levels of the ancillary metabolites serine and glycine compared to other thymic populations. In contrast, DP (CD4+CD8+) cells, characterized by low PKM2 expression and activity, displayed reduced levels of both glycolytic and TCA intermediates. Interestingly, despite having elevated PKM activity, SP8 (CD4-CD8+) cells mirrored the metabolic profile of DP cells, with similarly diminished glycolytic and TCA metabolite levels. |
| Institute: | National Cancer Institute |
| Department: | Center for Cancer Research |
| Laboratory: | Cancer Innovation Laboratory |
| Last Name: | Subleski |
| First Name: | Jeff |
| Address: | 1050 Boyles Street, Frederick, MD, 21713 |
| Email: | subleskj@mail.nih.gov |
| Phone: | 301-846-1515 |
Subject:
| Subject ID: | SU004617 |
| 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 source | thymocyte cell lines |
|---|---|---|---|
| SA527040 | 2-2 | T-cells | CD4+CD8+ |
| SA527041 | 2-6 | T-cells | CD4+CD8+ |
| SA527042 | 2-3 | T-cells | CD4+CD8+ |
| SA527043 | 2-5 | T-cells | CD4+CD8+ |
| SA527044 | 2-1 | T-cells | CD4+CD8+ |
| SA527045 | 2-4 | T-cells | CD4+CD8+ |
| SA527046 | 3-5 | T-cells | CD4+CD8- |
| SA527047 | 3-3 | T-cells | CD4+CD8- |
| SA527048 | 3-1 | T-cells | CD4+CD8- |
| SA527049 | 3-6 | T-cells | CD4+CD8- |
| SA527050 | 3-4 | T-cells | CD4+CD8- |
| SA527051 | 3-2 | T-cells | CD4+CD8- |
| SA527052 | 4-1 | T-cells | CD4-CD8+ |
| SA527053 | 4-3 | T-cells | CD4-CD8+ |
| SA527054 | 4-4 | T-cells | CD4-CD8+ |
| SA527055 | 4-5 | T-cells | CD4-CD8+ |
| SA527056 | 4-2 | T-cells | CD4-CD8+ |
| SA527057 | 4-6 | T-cells | CD4-CD8+ |
| SA527058 | 1-6 | T-cells | CD4-CD8- |
| SA527059 | 1-3 | T-cells | CD4-CD8- |
| SA527060 | 1-5 | T-cells | CD4-CD8- |
| SA527061 | 1-4 | T-cells | CD4-CD8- |
| SA527062 | 1-2 | T-cells | CD4-CD8- |
| SA527063 | 1-1 | T-cells | CD4-CD8- |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO004610 |
| Collection Summary: | Single cell suspension was made from mouse thymus by manual disruption in a Labplas FILTRA-BAG™ blender bag containing 5ml of cell isolation buffer (HBSS containing 0.1% BSA [Sigma-Aldrich] and 0.5 mM EDTA [Invitrogen]). Isolated thymocytes were stained in cell isolation buffer with live dead exclusion stain Sytox Green (ThermoFisher) and properly diluted monoclonal antibodies CD4-APC eflour 780 clone RM4-5 (ThermoFisher) and CD8a-BV421 clone 53-6.7 (Biolegend). Thymocytes were then sorted on a BD FACSAria by the Frederick National Laboratory Flow Cytometry Core. Cell populations were washed in PBS and cell pellets were snap frozen on dry ice/ethanol mixture. Samples were further processed and analyzed by West Coast Metabolomic Center (University of California, Davis). |
| Sample Type: | T-cells |
Treatment:
| Treatment ID: | TR004626 |
| Treatment Summary: | No treatments only 4 subsets of sorted thymocytes |
Sample Preparation:
| Sampleprep ID: | SP004623 |
| Sampleprep Summary: | See SOP-GCMS-02252019.pdf for details. Briefly, samples werevextracted using Matyash extraction procedure which includes MTBE, MeOH, and H2O. The aqueous (bottom) phase was dried down and submitted to derivatization for GC. |
| Sampleprep Protocol Filename: | SOP_GCMS-02252019.pdf |
Combined analysis:
| Analysis ID | AN007460 |
|---|---|
| Chromatography ID | CH005649 |
| MS ID | MS007152 |
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus IV TOF |
| Ion Mode | POSITIVE |
| Units | relative peak heights |
Chromatography:
| Chromatography ID: | CH005649 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min. |
| Flow Gradient: | NA |
| Flow Rate: | 1 mL/min |
| Solvent A: | NA |
| Solvent B: | NA |
| Chromatography Type: | GC |
MS:
| MS ID: | MS007152 |
| Analysis ID: | AN007460 |
| Instrument Name: | Leco Pegasus IV TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da. Blank QC and system sutability QC were run every 10 samples. These QC were not included in the curated report. |
| Ion Mode: | POSITIVE |
