Summary of Study ST004124

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 PR002592. The data can be accessed directly via it's Project DOI: 10.21228/M8M54Q 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 IDST004124
Study TitleDietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL22
Study SummaryThe mammalian small intestine is maintained by rapidly renewing Lgr5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. To explore the metabolic pathways influenced by cysteine in the small intestine and colon, we performed metabolomics analysis using high-pressure liquid chromatography-mass spectrometry (HPLC-MS) from the mice that were treated with control diet and cysteine-rich diet for 6 weeks. We found cysteine-rich diet significantly elevates the de novo Coenzyme A biosynthesis in the small intestine.
Institute
Massachusetts Institute of Technology
Last NameCHI
First NameFANGTAO
Address500 Main St building 76, Cambridge, MA 02139, USA.
Emailftchizju@gmail.com
Phone(617) 324-2577
Submit Date2025-08-19
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-09-11
Release Version1
FANGTAO CHI FANGTAO CHI
https://dx.doi.org/10.21228/M8M54Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002592
Project DOI:doi: 10.21228/M8M54Q
Project Title:Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL22
Project Summary:A fundamental question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues. The mammalian small intestine is maintained by rapidly renewing Lgr5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. To explore the metabolic pathways influenced by cysteine in the small intestine and colon, we performed metabolomics analysis using high-pressure liquid chromatography-mass spectrometry (HPLC-MS). Cysteine contributes to Coenzyme A (CoA) biosynthesis in intestinal epithelial cells, which promotes expansion of intraepithelial CD8αβ+ T cells and their production of interleukin-22 (IL-22). This enhanced IL-22 signaling directly augments ISCs reparative capacity after injury.
Institute:Koch Institute For Integrative Cancer Research at MIT
Last Name:CHI
First Name:FANGTAO
Address:500 Main St building 76, Cambridge, MA 02139, USA.
Email:ftchizju@gmail.com
Phone:(617) 324-2577

Subject:

Subject ID:SU004273
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 Treatment
SA476389SI-QC-blank2_posBlank Blank Blank
SA4763900318-SI-CD-QC-blank2_negBlank Blank Blank
SA4763910318-SI-CD-QC-blank2_posBlank Blank Blank
SA476392SI-iKO-QC-blank2_negBlank Blank Blank
SA476393SI-iKO-QC-blank2_posBlank Blank Blank
SA476394Col-QC-blank3_negBlank Blank Blank
SA476395SI-QC-blank2_negBlank Blank Blank
SA476396Col-QC-blank3_posBlank Blank Blank
SA476397Col-WTCD-4_negColon Wild-type Control
SA476398Col-WTCD-4_posColon Wild-type Control
SA476399Col-WTCD-1_posColon Wild-type Control
SA476400Col-WTCD-1_negColon Wild-type Control
SA476401Col-WTCD-5_posColon Wild-type Control
SA476402Col-WTCD-2_negColon Wild-type Control
SA476403Col-WTCD-3_posColon Wild-type Control
SA476404Col-WTCD-3_negColon Wild-type Control
SA476405Col-WTCD-2_posColon Wild-type Control
SA476406Col-WTCD-5_negColon Wild-type Control
SA476407Col-WTCysRD-4_posColon Wild-type CysRD
SA476408Col-WTCysRD-2_negColon Wild-type CysRD
SA476409Col-WTCysRD-1_negColon Wild-type CysRD
SA476410Col-WTCysRD-4_negColon Wild-type CysRD
SA476411Col-WTCysRD-1_posColon Wild-type CysRD
SA476412Col-WTCysRD-2_posColon Wild-type CysRD
SA476413Col-WTCysRD-5_negColon Wild-type CysRD
SA476414Col-WTCysRD-5_posColon Wild-type CysRD
SA476415Col-WTCysRD-3_posColon Wild-type CysRD
SA476416Col-WTCysRD-3_negColon Wild-type CysRD
SA4764170318-SI-iKOCD-5_posSmall Intestine Slc7a11-iKO Control
SA476418SI-iKO-CD-4_negSmall Intestine Slc7a11-iKO Control
SA476419SI-iKO-CD-1_posSmall Intestine Slc7a11-iKO Control
SA476420SI-iKO-CD-1_negSmall Intestine Slc7a11-iKO Control
SA476421SI-iKO-CD-2_posSmall Intestine Slc7a11-iKO Control
SA476422SI-iKO-CD-3_posSmall Intestine Slc7a11-iKO Control
SA476423SI-iKO-CD-3_negSmall Intestine Slc7a11-iKO Control
SA476424SI-iKO-CD-4_posSmall Intestine Slc7a11-iKO Control
SA476425SI-iKO-CD-5_negSmall Intestine Slc7a11-iKO Control
SA476426SI-iKO-CD-5_posSmall Intestine Slc7a11-iKO Control
SA4764270318-SI-iKOCD-4_negSmall Intestine Slc7a11-iKO Control
SA4764280318-SI-iKOCD-5_negSmall Intestine Slc7a11-iKO Control
SA4764290318-SI-iKOCD-1_negSmall Intestine Slc7a11-iKO Control
SA4764300318-SI-iKOCD-2_posSmall Intestine Slc7a11-iKO Control
SA4764310318-SI-iKOCD-2_negSmall Intestine Slc7a11-iKO Control
SA4764320318-SI-iKOCD-3_posSmall Intestine Slc7a11-iKO Control
SA4764330318-SI-iKOCD-3_negSmall Intestine Slc7a11-iKO Control
SA4764340318-SI-iKOCD-4_posSmall Intestine Slc7a11-iKO Control
SA4764350318-SI-iKOCD-1_posSmall Intestine Slc7a11-iKO Control
SA476436SI-iKO-CD-2_negSmall Intestine Slc7a11-iKO Control
SA476437SI-iKO-CysRD-5_negSmall Intestine Slc7a11-iKO CysRD
SA476438SI-iKO-CysRD-1_posSmall Intestine Slc7a11-iKO CysRD
SA476439SI-iKO-CysRD-5_posSmall Intestine Slc7a11-iKO CysRD
SA476440SI-iKO-CysRD-4_negSmall Intestine Slc7a11-iKO CysRD
SA476441SI-iKO-CysRD-4_posSmall Intestine Slc7a11-iKO CysRD
SA476442SI-iKO-CysRD-3_negSmall Intestine Slc7a11-iKO CysRD
SA476443SI-iKO-CysRD-3_posSmall Intestine Slc7a11-iKO CysRD
SA476444SI-iKO-CysRD-2_negSmall Intestine Slc7a11-iKO CysRD
SA476445SI-iKO-CysRD-1_negSmall Intestine Slc7a11-iKO CysRD
SA476446SI-iKO-CysRD-2_posSmall Intestine Slc7a11-iKO CysRD
SA476447SI-WTCD-5_posSmall Intestine Wild-type Control
SA476448SI-WTCD-1_posSmall Intestine Wild-type Control
SA4764490318-SI-WTCD-3_negSmall Intestine Wild-type Control
SA4764500318-SI-WTCD-3_posSmall Intestine Wild-type Control
SA4764510318-SI-WTCD-2_negSmall Intestine Wild-type Control
SA4764520318-SI-WTCD-2_posSmall Intestine Wild-type Control
SA4764530318-SI-WTCD-1_negSmall Intestine Wild-type Control
SA4764540318-SI-WTCD-1_posSmall Intestine Wild-type Control
SA476455SI-WTCD-6_posSmall Intestine Wild-type Control
SA476456SI-WTCD-6_negSmall Intestine Wild-type Control
SA4764570318-SI-WTCD-5_posSmall Intestine Wild-type Control
SA476458SI-WTCD-1_negSmall Intestine Wild-type Control
SA476459SI-WTCD-5_negSmall Intestine Wild-type Control
SA476460SI-WTCD-2_posSmall Intestine Wild-type Control
SA476461SI-WTCD-2_negSmall Intestine Wild-type Control
SA476462SI-WTCD-3_posSmall Intestine Wild-type Control
SA476463SI-WTCD-3_negSmall Intestine Wild-type Control
SA4764640318-SI-WTCD-4_negSmall Intestine Wild-type Control
SA476465SI-WTCD-4_posSmall Intestine Wild-type Control
SA476466SI-WTCD-4_negSmall Intestine Wild-type Control
SA476467SI-WTCD-7_posSmall Intestine Wild-type Control
SA476468SI-WTCD-7_negSmall Intestine Wild-type Control
SA4764690318-SI-WTCD-5_negSmall Intestine Wild-type Control
SA4764700318-SI-WTCD-4_posSmall Intestine Wild-type Control
SA476471SI-WTCysRD-6_negSmall Intestine Wild-type CysRD
SA476472SI-WTCysRD-7_posSmall Intestine Wild-type CysRD
SA476473SI-WTCysRD-1_posSmall Intestine Wild-type CysRD
SA476474SI-WTCysRD-1_negSmall Intestine Wild-type CysRD
SA476475SI-WTCysRD-2_posSmall Intestine Wild-type CysRD
SA476476SI-WTCysRD-2_negSmall Intestine Wild-type CysRD
SA476477SI-WTCysRD-3_posSmall Intestine Wild-type CysRD
SA476478SI-WTCysRD-3_negSmall Intestine Wild-type CysRD
SA476479SI-WTCysRD-4_posSmall Intestine Wild-type CysRD
SA476480SI-WTCysRD-4_negSmall Intestine Wild-type CysRD
SA476481SI-WTCysRD-5_posSmall Intestine Wild-type CysRD
SA476482SI-WTCysRD-5_negSmall Intestine Wild-type CysRD
SA476483SI-WTCysRD-7_negSmall Intestine Wild-type CysRD
SA476484SI-WTCysRD-6_posSmall Intestine Wild-type CysRD
Showing results 1 to 96 of 96

Collection:

Collection ID:CO004266
Collection Summary:The small intestine and colon tissues were rapidly excised, rinsed twice in 150mM ammonium acetate, and snap-frozen in liquid nitrogen. The snap-frozen tissues were homogenized to powder under liquid nitrogen with a pre-chilled mortar and pestle.
Sample Type:Intestine

Treatment:

Treatment ID:TR004282
Treatment Summary:Cysteine-rich diet (Research Diets, D21081608) was provided to male and female mice at the age of 8-12 weeks for 6 to 8 weeks. Control mice were provided a purified control diet (Research Diets, D12450J).

Sample Preparation:

Sampleprep ID:SP004279
Sampleprep Summary:About 20 mg of the tissue powder was used for metabolites extraction in 80% MeOH with OMNI bead homogenizer (OMNI, 19-628). The tissues/80%MeOH mixture was incubated for 24 hours at -80°C, spun at the top speed (16,000g) for 20 minutes at 4°C. The supernatants were transferred into new tubes and placed on ice. The sample pellets were resuspended in 500 μL 0.2M NaOH, heated at 95°C for 10 minutes, and the protein concentration was measured by BCA assay using 1:10 dilution. Finally, the 500 μg protein equivalent of MeOH supernatants were dried using multivap nitrogen evaporator. Dried metabolites were resuspended in 50% ACN:water at 50mg tissue extract/ml. 5 μL was loaded onto a Luna NH2 3 μm 100A (150 × 2.0 mm) column (Phenomenex) using a Vanquish Flex UPLC (Thermo Scientific).

Chromatography:

Chromatography ID:CH005193
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Luna NH2 (150 x 2.1 mm, 3 μm)
Column Temperature:27°C
Flow Gradient:0-17 min: 85% B - 5% B, 17-24 min: 5% B, 24-25 min: 5% B - 85% B, 25-36 min: 85% B.
Flow Rate:200 μL/min
Solvent A:100% Water; 5mM Ammonium acetate (pH 9.9)
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006837
Analysis Type:MS
Chromatography ID:CH005193
Num Factors:7
Num Metabolites:36
Units:Peak Intensity
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