Summary of Study ST002927
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 PR001819. The data can be accessed directly via it's Project DOI: 10.21228/M8KQ72 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 | ST002927 |
| Study Title | O-GlcNAcase activity maintains stress granules for proximity-enhanced ATP production to ensure recovery from stress |
| Study Summary | Accurate disassembly of stress granules (SGs) after environmental stimuli release is essential for cells to maintain homeostasis , which requires ATP-consuming processes. However, the molecular mechanism whereby regulation of SGs programmatically disassembly and ATP restoration remain poorly understood in mammalian cells. Here we found that defect of OGA in cells leads to aggregates formation, severe autophagy and eventually apoptosis during stress recovery. OGA, which localized in SGs, had no effect on SGs formation but could protect SGs from rapid disassembly during stress recovery stage. Then the SGs localized glycolysis-related enzymes were reserved and concentrated in SGs during stress release for ATP production in a proximity manner, which was vital to guarantee cells resistant to stress and survival during recovery. Finally, supplementation of ATP to OGA knockdown cells during stress recovery significantly rescue cell from aggregates, autophagy and apoptosis. Together, these results describe a brand new mechanism on how OGA regulates the programmed disassembly of stress granules and restoration of ATP to safeguard cell viability in a very precisely programmed process, whose rate is rigorous regulated. |
| Institute | Zhejiang University |
| Department | Life Sciences Institute |
| Laboratory | Shixian Lin |
| Last Name | Chen |
| First Name | Yulin |
| Address | Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang province, China |
| ychen209@qq.com | |
| Phone | 18868107794 |
| Submit Date | 2023-09-19 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-10-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001819 |
| Project DOI: | doi: 10.21228/M8KQ72 |
| Project Title: | O-GlcNAcase activity maintains stress granules for proximity-enhanced ATP production to ensure recovery from stress |
| Project Summary: | Accurate disassembly of stress granules (SGs) after environmental stimuli release is essential for cells to maintain homeostasis , which requires ATP-consuming processes. However, the molecular mechanism whereby regulation of SGs programmatically disassembly and ATP restoration remain poorly understood in mammalian cells. Here we found that defect of OGA in cells leads to aggregates formation, severe autophagy and eventually apoptosis during stress recovery. OGA, which localized in SGs, had no effect on SGs formation but could protect SGs from rapid disassembly during stress recovery stage. Then the SGs localized glycolysis-related enzymes were reserved and concentrated in SGs during stress release for ATP production in a proximity manner, which was vital to guarantee cells resistant to stress and survival during recovery. Finally, supplementation of ATP to OGA knockdown cells during stress recovery significantly rescue cell from aggregates, autophagy and apoptosis. Together, these results describe a brand new mechanism on how OGA regulates the programmed disassembly of stress granules and restoration of ATP to safeguard cell viability in a very precisely programmed process, whose rate is rigorous regulated. |
| Institute: | Zhejiang University |
| Department: | Life Sciences Institute |
| Laboratory: | Shixian Lin |
| Last Name: | Chen |
| First Name: | Yulin |
| Address: | Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang province, China |
| Email: | ychen209@qq.com |
| Phone: | 18868107794 |
Subject:
| Subject ID: | SU003040 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA317918 | C2 | noStressHeLa |
| SA317919 | C3 | noStressHeLa |
| SA317920 | C1 | noStressHeLa |
| SA317921 | C6 | noStressKDOGA |
| SA317922 | C5 | noStressKDOGA |
| SA317923 | C4 | noStressKDOGA |
| SA317903 | QC-1 | QC |
| SA317904 | QC-2 | QC |
| SA317905 | QC-3 | QC |
| SA317906 | C14 | RecoveryHeLa |
| SA317907 | C15 | RecoveryHeLa |
| SA317908 | C13 | RecoveryHeLa |
| SA317909 | C17 | RecoveryKDOGA |
| SA317910 | C16 | RecoveryKDOGA |
| SA317911 | C18 | RecoveryKDOGA |
| SA317912 | C9 | StressHeLa |
| SA317913 | C8 | StressHeLa |
| SA317914 | C7 | StressHeLa |
| SA317915 | C10 | StressKDOGA |
| SA317916 | C11 | StressKDOGA |
| SA317917 | C12 | StressKDOGA |
| Showing results 1 to 21 of 21 |
Collection:
| Collection ID: | CO003033 |
| Collection Summary: | Care was taken to quench cells quickly to minimize oxidation and degradation. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003049 |
| Treatment Summary: | HeLa cells of shControl or shOGA were treated with no stress, stress by 1 M sorbitol for 1 hr, or recovery from stress for 2 hr. |
Sample Preparation:
| Sampleprep ID: | SP003046 |
| Sampleprep Summary: | Briefly, equal confluency of cells in 6-well plate with 3 biological replicates were rinsed by 1 mL HPLC-grade water rapidly and immediately quenched by directly added by 1 mL liquid nitrogen to the plate. Then, 1 mL ice-cold 90% MC buffer (MC, 9: 1 MeOH: CHCl3. 90% MC, 9 : 1 MC: water) with 5 µM methionine sulfone as internal signal was added to each well of plate and the cells were scraped and transferred to1.5-mL tubes. Extracts were centrifuged at 4 ℃ for 5 min at 16,000 xg and the supernatants were transferred to new clean 1.5-mL tubes and equal volume of each sample was pooled for the QC sample. Finally, the extracts were dried using vacuum concentrator system and store at -80 ℃ until analysis. For targeted analysis, the dried extracts were resuspended by 100 µL 60% acetonitrile and centrifuged at 4 ℃ for 15 min at 15,000 xg after 30 min incubation at 4 ℃. Only the supernatant was transferred to autosampler vials for MS analysis. |
Combined analysis:
| Analysis ID | AN004800 | AN004801 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu 20AD | Shimadzu 20AD |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | QTRAP | QTRAP |
| MS instrument name | ABI Sciex Triple Quad 5500+ | ABI Sciex Triple Quad 5500+ |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak intensity | Peak intensity |
Chromatography:
| Chromatography ID: | CH003629 |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0.01 min 80% B, 20 min 20% B, 20.5 min 80% B, 24 min 80% B. |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 100% water, 20 mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004546 |
| Analysis ID: | AN004800 |
| Instrument Name: | ABI Sciex Triple Quad 5500+ |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | The raw data were extracted with the software Analyst v1.7.2 and OS v1.7. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004547 |
| Analysis ID: | AN004801 |
| Instrument Name: | ABI Sciex Triple Quad 5500+ |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | The raw data were extracted with the software Analyst v1.7.2 and OS v1.7. |
| Ion Mode: | NEGATIVE |
