Summary of Study ST004509

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 PR002838. The data can be accessed directly via it's Project DOI: 10.21228/M8TG2X This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST004509
Study TitleTargeted and untargeted metabolomics of wound bed derived macrophages
Study SummaryWhile in vitro studies have identified essential metabolites that can control inflammatory versus resolving macrophage phenotypes15, the factors that direct macrophages to resolve inflammation and promote repair in vivo are far less understood in part because of the newly appreciated heterogeneity of innate immune cells during tissue repair. Here, we sought to determine whether specific metabolites and metabolic pathways control inflammatory resolution in vivo. To identify metabolites that differ during macrophage resolution, we isolated F4/80+ macrophages from D1 and D3 wounds and performed global metabolic analysis, which measures ~600 key metabolites.
Institute
Yale University
Last NameCastano
First NameNicole
Address260 Whitney Ave, New Haven, Connecticut, 06511, USA
Emailnicole.castano@yale.edu
Phone7815728749
Submit Date2025-12-05
Raw Data AvailableYes
Raw Data File Type(s)mzML, wiff
Analysis Type DetailLC-MS
Release Date2026-01-19
Release Version1
Nicole Castano Nicole Castano
https://dx.doi.org/10.21228/M8TG2X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002838
Project DOI:doi: 10.21228/M8TG2X
Project Title:Glutamine metabolism tunes myeloid responses to drive resolution of inflammation during skin repair
Project Summary:Tissue repair requires inflammation resolution, but the molecular mechanisms involved in vivo are not fully understood. Here, we show that glutamine metabolism suppresses neutrophil recruitment to abrogate inflammation and drive skin wound repair. Integrated metabolomic and transcriptional profiling identified glutamine metabolism as enriched in macrophages during resolution. Dietary depletion studies and conditional deletion of glutaminase (Gls), the enzyme essential for glutamine metabolism, in mouse myeloid cells revealed that macrophages suppress neutrophil recruitment genes during tissue resolution to promote repair. We also found that these genes are upregulated in macrophages in patients with diabetes. Mechanistically, our data reveal that glutamine metabolism in macrophages induces suppressive chromatin remodeling of neutrophil recruitment genes, including Ccl ligands, during resolution of inflammation. These findings highlight the ability of specific metabolites to control cellular communication during tissue repair, with glutamine specifically to suppress neutrophil recruitment to advance inflammation resolution
Institute:Yale University
Department:Molecular Cellular and Developmental Biology
Laboratory:Horsley Lab
Last Name:Castano
First Name:Nicole
Address:260 Whitney Ave, New Haven, Connecticut, 06511, USA
Email:nicole.castano@yale.edu
Phone:7815728749

Subject:

Subject ID:SU004687
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 Factor
SA536582D1_Macrophage_2_RP_NegSkin Day 1 Wound Bed
SA536583D1_Macrophage_6_RP_PosSkin Day 1 Wound Bed
SA536584D1_Macrophage_5_RP_PosSkin Day 1 Wound Bed
SA536585D1_Macrophage_4_RP_PosSkin Day 1 Wound Bed
SA536586D1_Macrophage_3_RP_PosSkin Day 1 Wound Bed
SA536587D1_Macrophage_2_RP_PosSkin Day 1 Wound Bed
SA536588D1_Macrophage_1_RP_NegSkin Day 1 Wound Bed
SA536589D1_Macrophage_1_RP_PosSkin Day 1 Wound Bed
SA536590D1_Macrophage_6_RP_NegSkin Day 1 Wound Bed
SA536591D1_Macrophage_3_RP_NegSkin Day 1 Wound Bed
SA536592D1_Macrophage_5_RP_NegSkin Day 1 Wound Bed
SA536593D1_Macrophage_4_RP_NegSkin Day 1 Wound Bed
SA536594D3_Macrophage_1_RP_NegSkin Day 3 Wound Bed
SA536595D3_Macrophage_2_RP_NegSkin Day 3 Wound Bed
SA536596D3_Macrophage_6_RP_NegSkin Day 3 Wound Bed
SA536597D3_Macrophage_4_RP_NegSkin Day 3 Wound Bed
SA536598D3_Macrophage_5_RP_NegSkin Day 3 Wound Bed
SA536599D3_Macrophage_1_RP_PosSkin Day 3 Wound Bed
SA536600D3_Macrophage_2_RP_PosSkin Day 3 Wound Bed
SA536601D3_Macrophage_3_RP_PosSkin Day 3 Wound Bed
SA536602D3_Macrophage_4_RP_PosSkin Day 3 Wound Bed
SA536603D3_Macrophage_5_RP_PosSkin Day 3 Wound Bed
SA536604D3_Macrophage_6_RP_PosSkin Day 3 Wound Bed
SA536605D3_Macrophage_3_RP_NegSkin Day 3 Wound Bed
Showing results 1 to 24 of 24

Collection:

Collection ID:CO004680
Collection Summary:To avoid metabolic changes associated with FACS, macrophages were isolated from wound bed skin tissue using the anti-F4/80 MicroBeads UltraPure, mouse (Miltenyi Biotec, Catalog #130-110-443) according to the manufacturer’s protocol. Six wounds from 3 mice were pooled for each sample and a total of 6 samples were used for each timepoint. Wound bed tissue was excised, minced, and digested with Collagenase IA and Collagenase II to obtain a single-cell suspension.
Sample Type:Skin

Treatment:

Treatment ID:TR004696
Treatment Summary:After filtration through a 70-µm cell strainer to remove debris, cells were washed and resuspended in MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA). The single-cell suspension was incubated with anti-F4/80 MicroBeads for 15 minutes at 4°C. Labeled cells were then passed through an LS column (Miltenyi Biotec, Catalog #130-042-401) placed in a magnetic field using the QuadroMACS™ Separator (Miltenyi Biotec, Catalog #130-090-976) with MACS® MultiStand (Miltenyi Biotec, Catalog #130-042-303) according to manufacturer directions.

Sample Preparation:

Sampleprep ID:SP004693
Sampleprep Summary:Cells were quenched with 150 µL of ice-cold quenching buffer containing 20% methanol (MeOH), 0.1% formic acid, 3 mmol/L sodium fluoride (NaF), and 5.5 μg/mL D8-phenylalanine as an internal standard. The samples were then transferred to an LC-MS/MS V-bottom plate on dry ice and stored at –80°C until fully frozen. Once frozen, the samples were lyophilized overnight and then reconstituted in 50 µL of D4-taurine solution (25 μmol/L), which served as a second internal standard.

Combined analysis:

Analysis ID AN007560 AN007561
Chromatography ID CH005736 CH005736
MS ID MS007257 MS007258
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system SCIEX ExionLC SCIEX ExionLC
Column Phenomenex Kinetex C18 (100 x 2.1 mm, 2.6 µm) Phenomenex Kinetex C18 (100 x 2.1 mm, 2.6 µm)
MS Type EI EI
MS instrument type Triple TOF Triple TOF
MS instrument name ABI Sciex 6600 TripleTOF ABI Sciex 6600 TripleTOF
Ion Mode POSITIVE NEGATIVE
Units Arbitrary Units Arbitrary Units

Chromatography:

Chromatography ID:CH005736
Instrument Name:SCIEX ExionLC
Column Name:Phenomenex Kinetex C18 (100 x 2.1 mm, 2.6 µm)
Column Temperature:30°C
Flow Gradient:0 min, 0% B; 0.5 min, 0% B; 15 min, 100% B; 16 min, 100% B; 16.1 min, 0% B; and 20 min, 0%
Flow Rate:0.3 mL/min
Solvent A:95% Water/5% Acetonitrile; 0.1% formic acid
Solvent B:95% Acetonitrile/5% Water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS007257
Analysis ID:AN007560
Instrument Name:ABI Sciex 6600 TripleTOF
Instrument Type:Triple TOF
MS Type:EI
MS Comments:Data were analyzed using the Sciex TripleTOF 6600 using an information-dependent analysis (IDA) workflow consisting of a TOF MS scan (200 msec) and a high-resolution IDA experiment (70 msec each) monitoring 10 candidate ions per cycle. Former target ions were excluded after 2 occurrences for 5 sec and dynamic background subtraction was employed. The mass range for both TOF MS and IDA MS/MS scans was 60-1000. The ion source conditions were as follows: Ion spray voltage = 5000 V for positive mode, ion source gas 1 (GS1) = 50, ion source gas 2 (GS2) = 50, curtain gas (CUR) = 30, temperature (TEM) = 400oC. Compound dependent parameters for the two modes were: declustering potential (DP) = 35, collision energy (CE) = 30, collision energy spread (CES) = 20.
Ion Mode:POSITIVE
  
MS ID:MS007258
Analysis ID:AN007561
Instrument Name:ABI Sciex 6600 TripleTOF
Instrument Type:Triple TOF
MS Type:EI
MS Comments:Data were analyzed using the Sciex TripleTOF 6600 using an information-dependent analysis (IDA) workflow consisting of a TOF MS scan (200 msec) and a high-resolution IDA experiment (70 msec each) monitoring 10 candidate ions per cycle. Former target ions were excluded after 2 occurrences for 5 sec and dynamic background subtraction was employed. The mass range for both TOF MS and IDA MS/MS scans was 60-1000. The ion source conditions were as follows: Ion spray voltage = -4500 V for negative mode, ion source gas 1 (GS1) = 50, ion source gas 2 (GS2) = 50, curtain gas (CUR) = 30, temperature (TEM) = 400oC. Compound dependent parameters for the two modes were: declustering potential (DP) = 35, collision energy (CE) = 30, collision energy spread (CES) = 20.
Ion Mode:NEGATIVE
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