Summary of Study ST004215
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 PR002657. The data can be accessed directly via it's Project DOI: 10.21228/M86P0N 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 | ST004215 |
| Study Title | Intra-tumoral hypoxia promotes CD8+ T cell dysfunction via chronic activation of integrated stress response transcription factor ATF4 |
| Study Summary | This study investigates TME metabolic alterations in T cells caused by chronic expression of ATF4 in the context of antitumor immunity. T cells were isolated, extracted in 80% methanol, and subjected to untargeted metabolomic profiling by high-resolution LC–MS/MS. To test the role of chronic ATF4 in T cells we used four biological replicates were analyzed per group, including OT-1-ATF4Tg/Tg and OT-1-E8IcreATF4Tg/Tg. Samples were processed to quantify hydrophilic metabolites, normalized to protein content and total ion counts, and analyzed using statistical and pathway enrichment approaches. The resulting dataset provides a comprehensive profile of metabolic changes in tumor antigen–specific T cells and will support mechanistic studies on how transcriptional regulation and the tumor microenvironment influence T cell metabolism. Chronic ATF4 signaling led to robust increases in tricarboxylic acid (TCA) cycle intermediates and enforced unrestrained electron transport chain (ETC) activity, as indicated by reduced succinate:α-KG, fumarate:α-KG, and 2-HG:α-KG ratios. However, unchanged NADH:NAD ratios revealed a failure of complex I to keep pace with accelerated TCA metabolism. These findings demonstrate that sustained ATF4 activity promotes hyperactive mitochondrial metabolism, driving T cell exhaustion, mitochondrial defects, and apoptosis. |
| Institute | University of North Carolina at Chapel Hill |
| Last Name | Alicea Pauneto |
| First Name | Coral del Mar |
| Address | 5229 Marsico Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC |
| coraldm@ad.unc.edu | |
| Phone | (919) 966-9562 |
| Submit Date | 2025-09-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML,raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002657 |
| Project DOI: | doi: 10.21228/M86P0N |
| Project Title: | Intra-tumoral hypoxia promotes CD8+ T cell dysfunction via chronic activation of integrated stress response transcription factor ATF4 |
| Project Summary: | This study investigates TME metabolic alterations in T cells caused by chronic expression of ATF4 in the context of antitumor immunity. T cells were isolated, extracted in 80% methanol, and subjected to untargeted metabolomic profiling by high-resolution LC–MS/MS. To test the role of chronic ATF4 in T cells we used four biological replicates were analyzed per group, including OT-1-ATF4Tg/Tg and OT-1-E8IcreATF4Tg/Tg. Samples were processed to quantify hydrophilic metabolites, normalized to protein content and total ion counts, and analyzed using statistical and pathway enrichment approaches. The resulting dataset provides a comprehensive profile of metabolic changes in tumor antigen–specific T cells and will support mechanistic studies on how transcriptional regulation and the tumor microenvironment influence T cell metabolism. Chronic ATF4 signaling led to robust increases in tricarboxylic acid (TCA) cycle intermediates and enforced unrestrained electron transport chain (ETC) activity, as indicated by reduced succinate:α-KG, fumarate:α-KG, and 2-HG:α-KG ratios. However, unchanged NADH:NAD ratios revealed a failure of complex I to keep pace with accelerated TCA metabolism. These findings demonstrate that sustained ATF4 activity promotes hyperactive mitochondrial metabolism, driving T cell exhaustion, mitochondrial defects, and apoptosis. |
| Institute: | University of North Carolina at Chapel Hill |
| Department: | Pharmacology |
| Laboratory: | Thaxton Lab |
| Last Name: | Alicea Pauneto |
| First Name: | Coral del Mar |
| Address: | 5229 Marsico Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC |
| Email: | coraldm@ad.unc.edu |
| Phone: | (919) 966-9562 |
| Publications: | Immunity Cell Press |
| Contributors: | Coral del MarAlicea Pauneto, Brian P.Riesenberg, Evelyn J.Gandy, Andrew S.Kennedy, Genevieve T.Clutton, Jessica W.Hem, Katie E.Hurst, Elizabeth G.Hunt, Jarred M.Green, Brian C.Miller, Steven P. Angus, Gary L. Johnson, Robert J.Esther, Jennifer L. Guerriero,Peng Gao, David R.Soto-Pantoja, Robert L.Ferris, Jennifer L. Modliszewski,Michael F. Coleman, H Kay Chung, Justin Milner, Stergios J. Moschos,Luke Wiseman,Jessica E.Thaxton |
Subject:
| Subject ID: | SU004367 |
| 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 | Genotype |
|---|---|---|---|
| SA485747 | Tha-Kat-20250312-WT1 | T-Cells | OT1-ATF4 Tg/Tg |
| SA485748 | Tha-Kat-20250312-WT2 | T-Cells | OT1-ATF4 Tg/Tg |
| SA485749 | Tha-Kat-20250312-WT3 | T-Cells | OT1-ATF4 Tg/Tg |
| SA485750 | Tha-Kat-20250312-WT4 | T-Cells | OT1-ATF4 Tg/Tg |
| SA485751 | Tha-Kat-20250312-OE1 | T-Cells | OT1-E8IcreATF4 Tg/Tg |
| SA485752 | Tha-Kat-20250312-OE2 | T-Cells | OT1-E8IcreATF4 Tg/Tg |
| SA485753 | Tha-Kat-20250312-OE3 | T-Cells | OT1-E8IcreATF4 Tg/Tg |
| SA485754 | Tha-Kat-20250312-OE4 | T-Cells | OT1-E8IcreATF4 Tg/Tg |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO004360 |
| Collection Summary: | This dataset contains untargeted metabolomic profiles of T cells isolated from two experimental groups: OT-1-ATF4Tg/Tg and OT-1-E8IcreATF4Tg/Tg, with four biological replicates per group. T cells were harvested, extracted in 80% methanol, and analyzed using high-resolution LC–MS/MS. Metabolite abundances were normalized to total protein content and total ion counts, with missing values imputed and autoscaled to reduce heteroscedasticity. The dataset provides quantitative measurements of hydrophilic metabolites across experimental groups, enabling analysis of differential metabolite abundance and pathway enrichment in T cells under varying genetic backgrounds. |
| Sample Type: | T-cells |
| Collection Method: | T cells were isolated from mouse splenocytes and activated with CD3/28 beads |
Treatment:
| Treatment ID: | TR004376 |
| Treatment Summary: | n/a |
Sample Preparation:
| Sampleprep ID: | SP004373 |
| Sampleprep Summary: | T cells were harvested and washed with sodium chloride solution, then resuspended in 80% methanol. Samples underwent three freeze-thaw cycles at −80 °C and were stored at −20 °C overnight to precipitate hydrophilic metabolites. Following centrifugation at 20,000 × g, the methanol supernatant was collected for metabolite analysis. |
Chromatography:
| Chromatography ID: | CH005323 |
| Instrument Name: | Thermo Scientific UltiMate 3000 HPLC |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 0 min, 15% A; 2.5 min, 64% A; 12.4 min, 40% A; 12.5 min, 30% A; 12.5-14 min, 30% A; 14-21 min, 15% A. |
| Flow Rate: | 150 μL/min |
| Solvent A: | 95% water/5% acetonitrile; 20 mM ammonium hydroxide; 20 mM ammonium acetate, pH = 9.0 |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN007013 |
| Analysis Type: | MS |
| Chromatography ID: | CH005323 |
| Num Factors: | 2 |
| Num Metabolites: | 301 |
| Units: | total ion count |
