Summary of Study ST003067

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001913. The data can be accessed directly via it's Project DOI: 10.21228/M8FH9H This work is supported by NIH grant, U2C- DK119886.


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 IDST003067
Study TitleAttenuation of Helicobacter pylori VacA toxin-induced cell death by modulation of intracellular taurine metabolism - Study #1
Study Typeuntargeted metabolomics analysis
Study SummaryVacA alters the metabolite content of AGS cells. To detect potential VacA-induced metabolic alterations in host cells, we treated AGS cells with acid-activated VacA (20 μg/ml) or acidified buffer control for 2, 8, or 12 hours and performed untargeted global metabolic on the harvested cell pellets. AGS cells treated with VacA under these conditions do not undergo VacA-induced cell death. Analysis of the results showed that AGS cells treated with VacA had a significantly different metabolic profile than cells treated with an acidified-buffer control, both for RPLC and HILIC analyses.
Vanderbilt University
LaboratoryCenter for Innovative Technology
First NameSIMONA
Submit Date2024-02-02
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-06-12
Release Version1

Select appropriate tab below to view additional metadata details:


Project ID:PR001913
Project DOI:doi: 10.21228/M8FH9H
Project Title:Attenuation of Helicobacter pylori VacA toxin-induced cell death by modulation of intracellular taurine metabolism
Project Type:Untargeted Metabolomics analysis
Project Summary:Colonization of the human stomach with H. pylori strains producing active forms of a secreted toxin (VacA) is associated with an increased risk of peptic ulcer disease and gastric cancer, compared to colonization with strains producing hypoactive forms of VacA. Previous studies have shown that VacA causes cell vacuolation and mitochondrial dysfunction. In this study, we sought to define the cellular metabolic consequences of VacA intoxication. Untargeted metabolomic analyses revealed that several hundred metabolites were significantly altered in VacA-treated gastroduodenal cells (AGS and AZ-521) compared to control cells. Pathway analysis suggested that VacA caused alterations in taurine and hypotaurine metabolism. Treatment of cells with the purified active s1m1 form of VacA, but not hypoactive s2m1 or Delta_6-27 VacA mutant proteins (defective in membrane channel formation), caused reductions in taurine and hypotaurine levels. Supplementation of the tissue culture medium with taurine or hypotaurine protected AZ-521 cells against VacA-induced cell death. Untargeted global metabolomics of AZ-521 cells or AGS cells intoxicated with VacA in the presence or absence of extracellular taurine showed that taurine was the main intracellular metabolite significantly altered by extracellular taurine supplementation. These results indicate that VacA causes alterations in cellular taurine metabolism and indicate that repletion of taurine is sufficient to attenuate VacA-induced cell death.
Institute:Vanderbilt University
Laboratory:Center for Innovative Technology
First Name:SIMONA


Subject ID:SU003182
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:ATCC
Species Group:AGS and AZ-521


Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Treatment
SA332028rT12_1Control 12h
SA332029rT12_2Control 12h
SA332030rT12_3Control 12h
SA332031hT12_1Control 12h
SA332032hT12_2Control 12h
SA332033hT12_4Control 12h
SA332034hT12_3Control 12h
SA332035rT12_4Control 12h
SA332036hT2_4Control 2h
SA332037hT2_3Control 2h
SA332038hT2_2Control 2h
SA332039rT2_1Control 2h
SA332040hT2_1Control 2h
SA332041rT2_3Control 2h
SA332042rT2_2Control 2h
SA332043rT2_4Control 2h
SA332044rT8_1Control 8h
SA332045hT8_2Control 8h
SA332046hT8_3Control 8h
SA332047hT8_4Control 8h
SA332048hT8_1Control 8h
SA332049rT8_2Control 8h
SA332050rT8_3Control 8h
SA332051rT8_4Control 8h
SA332052hT12_7VacA 12h
SA332053hT12_8VacA 12h
SA332054rT12_8VacA 12h
SA332055rT12_5VacA 12h
SA332056hT12_6VacA 12h
SA332057hT12_5VacA 12h
SA332058rT12_7VacA 12h
SA332059rT12_6VacA 12h
SA332060rT2_6VacA 2h
SA332061rT2_5VacA 2h
SA332062hT2_8VacA 2h
SA332063hT2_5VacA 2h
SA332064rT2_7VacA 2h
SA332065rT2_8VacA 2h
SA332066hT2_7VacA 2h
SA332067hT2_6VacA 2h
SA332068rT8_5VacA 8h
SA332069rT8_6VacA 8h
SA332070rT8_8VacA 8h
SA332071hT8_6VacA 8h
SA332072hT8_7VacA 8h
SA332073hT8_5VacA 8h
SA332074hT8_8VacA 8h
SA332075rT8_7VacA 8h
Showing results 1 to 48 of 48


Collection ID:CO003175
Collection Summary:AGS cells or AZ-521 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum, or minimal essential medium (MEM) containing 10% fetal bovine serum and 5% nonessential amino acids, respectively.
Collection Protocol Filename:Cell_Culture_Methods.pdf
Sample Type:Stomach
Storage Conditions:-80℃


Treatment ID:TR003191
Treatment Summary:AGS and AZ-521 cells were cultured in T-75 cell culture flasks overnight to a density of approximately 4x106 cells. Cells were incubated in media containing 20 ug/mL of purified s1m1 VacA toxin and 5 mM ammonium chloride. Following intoxication, the media was removed, and cells were washed with PBS. Cells were detached by incubation with trypsin for 5 minutes and collected via centrifugation at 4°C at 1,000 rpm for 4 minutes. Trypsin was removed, cells were once again washed with PBS, and the cells were then flash-frozen in liquid nitrogen and stored at -70°C.
Treatment Protocol Filename:Cell_Culture_Methods.pdf

Sample Preparation:

Sampleprep ID:SP003188
Sampleprep Summary:Samples were analyzed via Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS and LC-HRMS/MS)-based metabolomics using previously described methods. Briefly, cell pellets were normalized by total protein (200 ug) and the corresponding cell supernatants were normalized by volume (200 uL). Metabolites were extracted with methanol/water 80:20. Heavy labeled phenylalanine-D8 and biotin-D2 were added to individual samples prior to protein precipitation. Following overnight incubation at -80°C, precipitated proteins were pelleted by centrifugation at 10,000 rpm for 10 min and metabolite extracts were transferred into two Eppendorf tubes in equal amounts and dried down in vacuo and stored at -80°C.
Sampleprep Protocol Filename:MS_Methods.pdf
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN005023 AN005024
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um) Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Units time_m/z time_m/z


Chromatography ID:CH003795
Methods Filename:MS_Methods.pdf
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
Column Temperature:40
Flow Gradient:30 min; 95%A, 5%B
Flow Rate:0.25 mL/min
Solvent A:100% water, 0.1% Formic Acid
Solvent B:80:20 acetonitrile:water, 0.1% Formic Acid
Chromatography Type:Reversed phase
Chromatography ID:CH003796
Methods Filename:MS_Methods.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
Column Temperature:30
Flow Gradient:30 min; 5%A, 95%B
Flow Rate:0.20 mL/min
Solvent A:90% water, 10% acetonitrile, 5mM Ammonium Formate, 0.1%FA
Solvent B:10% water, 90% acetonitrile, 5mM Ammonium Formate, 0.1%FA
Chromatography Type:HILIC


MS ID:MS004762
Analysis ID:AN005023
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Comments:Mass spectrometry raw data was imported, processed, normalized, and reviewed using Progenesis QI v.3.0 (Non-linear Dynamics, Newcastle, UK).
MS ID:MS004763
Analysis ID:AN005024
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Comments:Mass spectrometry raw data was imported, processed, normalized, and reviewed using Progenesis QI v.3.0 (Non-linear Dynamics, Newcastle, UK).