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.

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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.

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Study IDST002927
Study TitleO-GlcNAcase activity maintains stress granules for proximity-enhanced ATP production to ensure recovery from stress
Study SummaryAccurate 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
DepartmentLife Sciences Institute
LaboratoryShixian Lin
Last NameChen
First NameYulin
AddressLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang province, China
Emailychen209@qq.com
Phone18868107794
Submit Date2023-09-19
Raw Data AvailableYes
Raw Data File Type(s)mzML, wiff
Analysis Type DetailLC-MS
Release Date2023-10-14
Release Version1
Yulin Chen Yulin Chen
https://dx.doi.org/10.21228/M8KQ72
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA317918C2noStressHeLa
SA317919C3noStressHeLa
SA317920C1noStressHeLa
SA317921C6noStressKDOGA
SA317922C5noStressKDOGA
SA317923C4noStressKDOGA
SA317903QC-1QC
SA317904QC-2QC
SA317905QC-3QC
SA317906C14RecoveryHeLa
SA317907C15RecoveryHeLa
SA317908C13RecoveryHeLa
SA317909C17RecoveryKDOGA
SA317910C16RecoveryKDOGA
SA317911C18RecoveryKDOGA
SA317912C9StressHeLa
SA317913C8StressHeLa
SA317914C7StressHeLa
SA317915C10StressKDOGA
SA317916C11StressKDOGA
SA317917C12StressKDOGA
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 Triple quadrupole Triple quadrupole
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:Triple quadrupole
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:Triple quadrupole
MS Type:ESI
MS Comments:The raw data were extracted with the software Analyst v1.7.2 and OS v1.7.
Ion Mode:NEGATIVE
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