Summary of Study ST003265
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 PR002027. The data can be accessed directly via it's Project DOI: 10.21228/M8M24P 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 | ST003265 |
| Study Title | Malic Enzyme 2 maintains metabolic state and anti-tumor immunity of CD8+ T cells |
| Study Summary | For metabolite analysis, naive ME2+/+ and ME2-/- CD8+ T cells were isolated and activated with anti-CD3 (4μg/ml) and anti-CD28 (1μg/ml). Cells were washed twice with ice-cold PBS and metabolites were extracted with ice-cold 80% methanol. The extracts were analyzed by LC-MS/MS. |
| Institute | Peking Union Medical College |
| Last Name | zhang |
| First Name | zhenxi |
| Address | Beijing Dongdan Santiao No.5 |
| 13121716766@163.com | |
| Phone | 69156953 |
| Submit Date | 2024-06-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002027 |
| Project DOI: | doi: 10.21228/M8M24P |
| Project Title: | Malic Enzyme 2 maintains metabolic state and anti-tumor immunity of CD8+ T cells |
| Project Summary: | The functional integrity of CD8+ T cells is closely linked to metabolic reprogramming, therefore, understanding of the metabolic basis of CD8+ T cell activation and antitumor immunity could provide insights into tumor immunotherapy. Here, we report that ME2 is critical for CD8+ T cell activation and immune response against malignancy. ME2 deficiency suppresses CD8+ T cells activation and anti-tumor immune response in vitro and in vivo. Mechanistically, ME2 depletion blocks the TCA cycle flux, leading to the accumulation of fumarate. Fumarate directly binds to DAPK1 and inhibits its activity by competing with ATP for binding. Notably, ME2 deficiency increases the ratio of fumarate to ATP, thereby leading to the inhibition of DAPK1. Consistently, pharmacological inhibition of DAPK1 abolishes the anti-tumor function conferred by ME2 to CD8+ T cells. Collectively, these findings demonstrate a role for ME2 in the regulation of CD8+ T cell metabolism and effector functions, as well as an unexpected function for fumarate as a metabolic signal in the inhibition of DAPK1. |
| Institute: | Peking Union Medical College |
| Last Name: | zhenxi |
| First Name: | zhang |
| Address: | Beijing Dongdan Santiao No.5 |
| Email: | 13121716766@163.com |
| Phone: | 010-69156953 |
Subject:
| Subject ID: | SU003385 |
| 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 | Sample source |
|---|---|---|---|
| SA354268 | KO3 | Me2-knockout | CD8 T cell |
| SA354269 | K3 | Me2-knockout | CD8 T cell |
| SA354270 | K2 | Me2-knockout | CD8 T cell |
| SA354271 | K1 | Me2-knockout | CD8 T cell |
| SA354272 | KO5 | Me2-knockout | CD8 T cell |
| SA354273 | KO4 | Me2-knockout | CD8 T cell |
| SA354274 | KO2 | Me2-knockout | CD8 T cell |
| SA354275 | KO1 | Me2-knockout | CD8 T cell |
| SA354276 | WT2 | wild-type | CD8 T cell |
| SA354277 | W1 | wild-type | CD8 T cell |
| SA354278 | W2 | wild-type | CD8 T cell |
| SA354279 | W3 | wild-type | CD8 T cell |
| SA354280 | WT5 | wild-type | CD8 T cell |
| SA354281 | WT4 | wild-type | CD8 T cell |
| SA354282 | WT3 | wild-type | CD8 T cell |
| SA354283 | WT1 | wild-type | CD8 T cell |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO003378 |
| Collection Summary: | Mouse CD8+ T cells were isolated from the spleen and lymph nodes of ME2 wild-type and ME2 knockout mice (knockdown of ME2 in T cells). The mice were euthanized and soaked in 75% alcohol for 3 minutes. Separate mouse spleens using a dissector and grind them into single-cell suspensions using a grinder. Single-cell suspension was used for CD8+ T cell isolation using the Mouse Lymphocyte Isolation Kit (Biolegend, 480044, China). T cells were cultured in RMPI-1640 medium supplemented with 10% FBS, 10μg/ml β-mercaptoethanol, and 1% penicillin and streptomycin. For metabolite analysis, CD8+ T cells were stimulated with 4 μg/ml anti-CD3 and 1μg/ml anti-CD28 antibodies for 24 h. |
| Sample Type: | T-cells |
| Storage Conditions: | On ice |
Treatment:
| Treatment ID: | TR003394 |
| Treatment Summary: | Naive ME2+/+ and ME2-/- CD8+ T cells were isolated and activated with anti-CD3 (4μg/ml) and anti-CD28 (1μg/ml). |
Sample Preparation:
| Sampleprep ID: | SP003392 |
| Sampleprep Summary: | For metabolite analysis, naive ME2+/+ and ME2-/- CD8+ T cells were isolated and activated with anti-CD3 (4μg/ml) and anti-CD28 (1μg/ml). Cells were washed twice with ice-cold PBS and metabolites were extracted with ice-cold 80% methanol. The extracts were analyzed by LC-MS/MS. |
| Extraction Method: | Cells were washed twice with ice-cold PBS and metabolites were extracted with ice-cold 80% methanol. |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN005349 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Focus |
| Ion Mode | UNSPECIFIED |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH004051 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 35 |
| Flow Gradient: | 0-2 min, 100% phase A; 2-11 min, 0% to 100% B; 11-13 min, 100% B; 13-15 min, 0% to 100% A. |
| Flow Rate: | 0.4 ml/min |
| Solvent A: | 100% water; 0.1 % formic acid |
| Solvent B: | 100% methanol; 0.1 % formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005079 |
| Analysis ID: | AN005349 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Q Exactive mass spectrometer was operated in full MS and polarity switching mode (acquisition from m/z 50 to 500) with a scan resolution set at 35,000. Five independent cell cultures were measured for each condition and samples were randomised in order to avoid bias in sample analyses due to machine drift. Q Exactive LC-MS/MS vendor raw data files were converted to the open source format mzML using the program ProteoWizard, and then the XCMS program was used for peak alignment, retention time correction and peak area extraction. Significance was determined using an unpaired Student's t-test. p-value < 0.05 was considered as statistically significant. The acquired spectra were analysed using XCalibur Qual Browser and XCalibur Quan Browser software (Thermo Scientific) by referencing to an internal library of compounds. |
| Ion Mode: | UNSPECIFIED |
