Summary of Study ST003405
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 PR002104. The data can be accessed directly via it's Project DOI: 10.21228/M8NJ9Q 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 | ST003405 |
| Study Title | Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis |
| Study Summary | The integrated stress response (ISR) enables cells to cope with a variety of insults, but its specific contribution to downstream cellular outputs remains unclear. Using a synthetic tool, we selectively activate the ISR without co-activation of parallel pathways and define the resulting cellular state with multi-omics profiling. We identify time- and dose-dependent gene expression modules, with ATF4 driving only a small but sensitive subgroup that includes amino acid metabolic enzymes. This ATF4 response affects cellular bioenergetics, rerouting carbon utilization towards amino acid production and away from the tricarboxylic acid cycle and fatty acid synthesis. We also find an ATF4-independent reorganization of the lipidome that promotes DGAT-dependent triglyceride synthesis and accumulation of lipid droplets. While DGAT1 is the main driver of lipid droplet biogenesis, DGAT2 plays an essential role in buffering stress and maintaining cell survival. Together, we demonstrate the sufficiency of the ISR in promoting a previously unappreciated metabolic state. |
| Institute | Calico Life Sciences |
| Last Name | Bryan |
| First Name | King |
| Address | 1170 Veterans Blvd, South San Francisco, CA 94080 |
| bryan@calicolabs.com | |
| Phone | (650) 754-6200 |
| Submit Date | 2024-08-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002104 |
| Project DOI: | doi: 10.21228/M8NJ9Q |
| Project Title: | Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis |
| Project Type: | Biology |
| Project Summary: | The integrated stress response (ISR) enables cells to cope with a variety of insults, but its specific contribution to downstream cellular outputs remains unclear. Using a synthetic tool, we selectively activate the ISR without co-activation of parallel pathways and define the resulting cellular state with multi-omics profiling. We identify time- and dose-dependent gene expression modules, with ATF4 driving only a small but sensitive subgroup that includes amino acid metabolic enzymes. This ATF4 response affects cellular bioenergetics, rerouting carbon utilization towards amino acid production and away from the tricarboxylic acid cycle and fatty acid synthesis. We also find an ATF4-independent reorganization of the lipidome that promotes DGAT-dependent triglyceride synthesis and accumulation of lipid droplets. While DGAT1 is the main driver of lipid droplet biogenesis, DGAT2 plays an essential role in buffering stress and maintaining cell survival. Together, we demonstrate the sufficiency of the ISR in promoting a previously unappreciated metabolic state. |
| Institute: | Calico Life Sciences |
| Department: | Department of Mass Spectrometry-Technology Lab |
| Laboratory: | Metabolomics Lab |
| Last Name: | Vu |
| First Name: | Ngoc |
| Address: | 1130 Veterans BLVD, South San Francisco, CA 94080 |
| Email: | ngochmvu@gmail.com |
| Phone: | 6504205430 |
| Publications: | Labbe, Lebon & King et al., Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis.Nat Comm.2024 |
Subject:
| Subject ID: | SU003530 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | ATF4 | Treatment_time |
|---|---|---|---|---|
| SA371943 | KO_0h_supp_1 | U2OS Osteosarcoma Cell Line | KO | 0 |
| SA371944 | KO_0h_supp_2 | U2OS Osteosarcoma Cell Line | KO | 0 |
| SA371945 | KO_0h_supp_3 | U2OS Osteosarcoma Cell Line | KO | 0 |
| SA371946 | KO_30m_supp_1 | U2OS Osteosarcoma Cell Line | KO | 0.5 |
| SA371947 | KO_30m_supp_2 | U2OS Osteosarcoma Cell Line | KO | 0.5 |
| SA371948 | KO_30m_supp_3 | U2OS Osteosarcoma Cell Line | KO | 0.5 |
| SA371949 | KO_24h_supp_3 | U2OS Osteosarcoma Cell Line | KO | 24 |
| SA371950 | KO_24h_supp_2 | U2OS Osteosarcoma Cell Line | KO | 24 |
| SA371951 | KO_24h_supp_1 | U2OS Osteosarcoma Cell Line | KO | 24 |
| SA371952 | KO_4h_supp_2 | U2OS Osteosarcoma Cell Line | KO | 4 |
| SA371953 | KO_4h_supp_3 | U2OS Osteosarcoma Cell Line | KO | 4 |
| SA371954 | KO_4h_supp_1 | U2OS Osteosarcoma Cell Line | KO | 4 |
| SA371955 | KO_8h_supp_2 | U2OS Osteosarcoma Cell Line | KO | 8 |
| SA371956 | KO_8h_supp_1 | U2OS Osteosarcoma Cell Line | KO | 8 |
| SA371957 | KO_8h_supp_3 | U2OS Osteosarcoma Cell Line | KO | 8 |
| SA371958 | WT_0h_supp_3 | U2OS Osteosarcoma Cell Line | WT | 0 |
| SA371959 | WT_0h_supp_1 | U2OS Osteosarcoma Cell Line | WT | 0 |
| SA371960 | WT_0h_supp_2 | U2OS Osteosarcoma Cell Line | WT | 0 |
| SA371961 | WT_30m_supp_3 | U2OS Osteosarcoma Cell Line | WT | 0.5 |
| SA371962 | WT_30m_supp_2 | U2OS Osteosarcoma Cell Line | WT | 0.5 |
| SA371963 | WT_30m_supp_1 | U2OS Osteosarcoma Cell Line | WT | 0.5 |
| SA371964 | WT_24h_supp_1 | U2OS Osteosarcoma Cell Line | WT | 24 |
| SA371965 | WT_24h_supp_2 | U2OS Osteosarcoma Cell Line | WT | 24 |
| SA371966 | WT_24h_supp_3 | U2OS Osteosarcoma Cell Line | WT | 24 |
| SA371967 | WT_4h_supp_3 | U2OS Osteosarcoma Cell Line | WT | 4 |
| SA371968 | WT_4h_supp_1 | U2OS Osteosarcoma Cell Line | WT | 4 |
| SA371969 | WT_4h_supp_2 | U2OS Osteosarcoma Cell Line | WT | 4 |
| SA371970 | WT_8h_supp_1 | U2OS Osteosarcoma Cell Line | WT | 8 |
| SA371971 | WT_8h_supp_2 | U2OS Osteosarcoma Cell Line | WT | 8 |
| SA371972 | WT_8h_supp_3 | U2OS Osteosarcoma Cell Line | WT | 8 |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO003523 |
| Collection Summary: | Cells were washed with room temperature PBS followed by quenching in 80% methanol containing internal standards (D4-L-tyrosine, 15N4-L-arginine and D5-benzoic acid; Sigma-Aldrich) maintained at -20℃. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003539 |
| Treatment Summary: | Cells were treated with 0.05 nM AP20187 spiked into media at indicated timepoint to activate dimerizable PERK prior to harvest. For 0h timepoint, cells were treated with vehicle (ethanol). |
Sample Preparation:
| Sampleprep ID: | SP003537 |
| Sampleprep Summary: | Cells were scraped, transferred to microcentrifuge tubes, then centrifuged at 16,000 x g at 4℃ for 15 min. Supernatants were dried down under nitrogen at 4℃. Dried extracts were resuspended at 5x concentration in 40% methanol/40% acetonitrile/20% water containing additional standards (D5-L-phenylalanine, D4-L-lysine and D5-succinate; Sigma-Aldrich). |
Combined analysis:
| Analysis ID | AN005588 | AN005589 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | log2 peak area top | log2 peak area top |
Chromatography:
| Chromatography ID: | CH004247 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 37℃ |
| Flow Gradient: | t = −6, 84.2% B; t = 0, 84.2% B; t = 2.5, 76.8% B; t = 5, 68.4% B, t = 7.5, 60% B; t = 10, 52.6% B; t = 15, 36.8% B; t = 20; 21% B; t = 22, 15.8% B; t = 22.5, 84.2% B; t = 24; 84.2% B. |
| Flow Rate: | 150 μL/min |
| Solvent A: | 100% Water; 20 mM ammonium carbonate (pH 9.2) |
| Solvent B: | 95% Acetonitrile/5% Solvent A |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005313 |
| Analysis ID: | AN005588 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data was acquired using data-dependent acquisition (DDA) mode with the following parameters: resolution = 70,000, AGC target = 3.00 × 10 maximum IT (ms) = 100, scan range = 70–1050. The MS2 parameters were as follows: resolution = 17,500, AGC target = 1.00 × 105, maximum IT (ms) = 50, loop count = 6, isolation window (m/z) = 1, (N)CE = 20, 40, 80; underfill ratio = 1.00%, Apex trigger(s) = 3–10, dynamic exclusion(s) = 25. (N)CE = 20, 50, 100. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005314 |
| Analysis ID: | AN005589 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data was acquired using data-dependent acquisition (DDA) mode with the following parameters: resolution = 70,000, AGC target = 3.00 × 10 maximum IT (ms) = 100, scan range = 70–1050. The MS2 parameters were as follows: resolution = 17,500, AGC target = 1.00 × 105, maximum IT (ms) = 50, loop count = 6, isolation window (m/z) = 1, (N)CE = 20, 40, 80; underfill ratio = 1.00%, Apex trigger(s) = 3–10, dynamic exclusion(s) = 25. (N)CE = 20, 50, 100. |
| Ion Mode: | NEGATIVE |
