Summary of Study ST003135

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 PR001948. The data can be accessed directly via it's Project DOI: 10.21228/M8XF0R 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.

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Study IDST003135
Study TitleMetabolomic study of T effector and T regulatory cells in severe allergic patients
Study SummaryMetabolism has a profound impact on T cell fate and function. Uncovering the metabolome of circulating human CD4+ T effector memory (Teff) and T regulatory (Treg) cells would enable better understanding of Th2-driven diseases, such as allergy or asthma. Here, we demonstrated that in healthy humans, energy metabolism and functions of memory CD4+ Teff cells mainly relied on amino acids, whereas Treg cells predominantly used fatty acids. Arginine and phenylalanine increased T cell receptorinduced glycolysis and oxidative phosphorylation in total and memory CD4+ T cells, but high levels of phenylalanine limited CD4+ T cell proliferation via disrupting mitochondrial respiration and activation of L-phenylalanine oxidase, IL4I1. Accordingly, lowest levels of phenylalanine were linked with the pathogenic Th2a cells, and impaired Treg cells in patients with the most severe forms of allergies. It all suggests that phenylalanine is a metabolic checkpoint of pathogenic Th2 cells development.
Institute
Universidad CEU San Pablo
DepartmentQuímica y Bioquímica
Last NameVillaseñor
First NameAlma
AddressUrbanización Montepríncipe, n/s, Boadilla del Monte, Madrid, 28003, Spain
Emailalma.villasenor@ceu.es
Phone913724750
Submit Date2024-02-22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-08-22
Release Version1
Alma Villaseñor Alma Villaseñor
https://dx.doi.org/10.21228/M8XF0R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001948
Project DOI:doi: 10.21228/M8XF0R
Project Title:Metabolomic study of T effector and T regulatory cells in severe allergic patients
Project Type:MS untargeted analysis combining lipidomics and metabolomics.
Project Summary:Metabolism has a profound impact on T cell fate and function. Uncovering the metabolome of circulating human CD4+ T effector memory (Teff) and T regulatory (Treg) cells would enable better understanding of Th2-driven diseases, such as allergy or asthma. Here, we demonstrated that in healthy humans, energy metabolism and functions of memory CD4+ Teff cells mainly relied on amino acids, whereas Treg cells predominantly used fatty acids. Arginine and phenylalanine increased T cell receptorinduced glycolysis and oxidative phosphorylation in total and memory CD4+ T cells, but high levels of phenylalanine limited CD4+ T cell proliferation via disrupting mitochondrial respiration and activation of L-phenylalanine oxidase, IL4I1. Accordingly, lowest levels of phenylalanine were linked with the pathogenic Th2a cells, and impaired Treg cells in patients with the most severe forms of allergies. It all suggests that phenylalanine is a metabolic checkpoint of pathogenic Th2 cells development.
Institute:Universidad CEU San Pablo
Department:Química y Bioquímica
Last Name:Villaseñor
First Name:Alma
Address:Urbanización Montepríncipe, n/s, Boadilla del Monte, Madrid, 28003, Spain
Email:alma.villasenor@ceu.es
Phone:913724750

Subject:

Subject ID:SU003252
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Adult patients (>18 years old)
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Experimental_Group Cell_Type
SA339354Blank_Eff_PolarBlank Teff
SA339355Blank_Eff_LipidsBlank Teff
SA339356Blank_Reg_PolarBlank Treg
SA339357Blank_Reg_LipidsBlank Treg
SA339358Curve_1500_Eff_LipidsCell_Curve Teff
SA339359Curve_500_Eff_LipidsCell_Curve Teff
SA339360Curve_100_Eff_LipidsCell_Curve Teff
SA339361Curve_250_Eff_PolarCell_Curve Teff
SA339362Curve_250_Eff_LipidsCell_Curve Teff
SA339363Curve_500_Eff_PolarCell_Curve Teff
SA339364Curve_1500_Eff_PolarCell_Curve Teff
SA339365Curve_100_Eff_PolarCell_Curve Teff
SA339366Curve_50_Reg_LipidsCell_Curve Treg
SA339367Curve_100_Reg_PolarCell_Curve Treg
SA339368Curve_50_Reg_PolarCell_Curve Treg
SA339369Curve_25_Reg_LipidsCell_Curve Treg
SA339370Curve_10_Reg_PolarCell_Curve Treg
SA339371Curve_10_Reg_LipidsCell_Curve Treg
SA339372Curve_100_Reg_LipidsCell_Curve Treg
SA339373Curve_25_Reg_PolarCell_Curve Treg
SA339374B2_Eff_LipidsMild Teff
SA339375B3_Eff_PolarMild Teff
SA339376B4_Eff_PolarMild Teff
SA339377B2_Eff_PolarMild Teff
SA339378B3_Eff_LipidsMild Teff
SA339379B4_Eff_LipidsMild Teff
SA339380B4_Reg_PolarMild Treg
SA339381B3_Reg_LipidsMild Treg
SA339382B4_Reg_LipidsMild Treg
SA339383B3_Reg_PolarMild Treg
SA339384B2_Reg_PolarMild Treg
SA339385B2_Reg_LipidsMild Treg
SA339386A4_Eff_PolarNon_Allergic Teff
SA339387A4_Eff_LipidsNon_Allergic Teff
SA339388A7_Eff_PolarNon_Allergic Teff
SA339389A7_Eff_LipidsNon_Allergic Teff
SA339390A8_Eff_PolarNon_Allergic Teff
SA339391A5_Eff_PolarNon_Allergic Teff
SA339392A2_Eff_LipidsNon_Allergic Teff
SA339393A6_Eff_LipidsNon_Allergic Teff
SA339394A2_Eff_PolarNon_Allergic Teff
SA339395A8_Eff_LipidsNon_Allergic Teff
SA339396A6_Eff_PolarNon_Allergic Teff
SA339397A5_Eff_LipidsNon_Allergic Teff
SA339398A6_Reg_PolarNon_Allergic Treg
SA339399A7_Reg_PolarNon_Allergic Treg
SA339400A7_Reg_LipidsNon_Allergic Treg
SA339401A6_Reg_LipidsNon_Allergic Treg
SA339402A8_Reg_PolarNon_Allergic Treg
SA339403A4_Reg_PolarNon_Allergic Treg
SA339404A5_Reg_PolarNon_Allergic Treg
SA339405A8_Reg_LipidsNon_Allergic Treg
SA339406A4_Reg_LipidsNon_Allergic Treg
SA339407A5_Reg_LipidsNon_Allergic Treg
SA339408A2_Reg_LipidsNon_Allergic Treg
SA339409A2_Reg_PolarNon_Allergic Treg
SA339410QC15_Eff_PolarQuality_Control Teff
SA339411QC15_Eff_LipidsQuality_Control Teff
SA339412QC16_Eff_PolarQuality_Control Teff
SA339413QC14_Eff_LipidsQuality_Control Teff
SA339414QC14_Eff_PolarQuality_Control Teff
SA339415QC13_Eff_PolarQuality_Control Teff
SA339416QC12_Eff_PolarQuality_Control Teff
SA339417QC13_Eff_LipidsQuality_Control Teff
SA339418QC16_Eff_LipidsQuality_Control Teff
SA339419QC21_Eff_PolarQuality_Control Teff
SA339420QC20_Eff_PolarQuality_Control Teff
SA339421QC20_Eff_LipidsQuality_Control Teff
SA339422QC21_Eff_LipidsQuality_Control Teff
SA339423QC17_Eff_PolarQuality_Control Teff
SA339424QC19_Eff_LipidsQuality_Control Teff
SA339425QC12_Eff_LipidsQuality_Control Teff
SA339426QC17_Eff_LipidsQuality_Control Teff
SA339427QC19_Eff_PolarQuality_Control Teff
SA339428QC18_Eff_PolarQuality_Control Teff
SA339429QC18_Eff_LipidsQuality_Control Teff
SA339430QC8_Reg_LipidsQuality_Control Treg
SA339431QC7_Reg_PolarQuality_Control Treg
SA339432QC7_Reg_LipidsQuality_Control Treg
SA339433QC8_Reg_PolarQuality_Control Treg
SA339434QC9_Reg_LipidsQuality_Control Treg
SA339435QC6_Reg_LipidsQuality_Control Treg
SA339436QC10_Reg_LipidsQuality_Control Treg
SA339437QC10_Reg_PolarQuality_Control Treg
SA339438QC9_Reg_PolarQuality_Control Treg
SA339439QC3_Reg_LipidsQuality_Control Treg
SA339440QC2_Reg_LipidsQuality_Control Treg
SA339441QC2_Reg_PolarQuality_Control Treg
SA339442QC1_Reg_LipidsQuality_Control Treg
SA339443QC1_Reg_PolarQuality_Control Treg
SA339444QC3_Reg_PolarQuality_Control Treg
SA339445QC4_Reg_PolarQuality_Control Treg
SA339446QC5_Reg_LipidsQuality_Control Treg
SA339447QC5_Reg_PolarQuality_Control Treg
SA339448QC4_Reg_LipidsQuality_Control Treg
SA339449QC6_Reg_PolarQuality_Control Treg
SA339450C12_Eff_PolarSevere Teff
SA339451C6_Eff_PolarSevere Teff
SA339452C9_Eff_LipidsSevere Teff
SA339453C10_Eff_PolarSevere Teff
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Collection:

Collection ID:CO003245
Collection Summary:Whole blood was drawn from the participants into heparin tubes and serum in silica tubes. Next, PBMCs were isolated using Ficoll Plaque by gradient density centrifugation according to manufacturer instructions. Isolated PMBCs were then immediately frozen and kept at -80˚C until analysis. Teff and Treg cell subpopulations were determined through FlowJo X (v.10.7.1.) and FlowSOM (v.2.6).
Sample Type:Blood (whole)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003261
Treatment Summary:After cell sorting, the only treatment received was the addition of a volume of 50 uL of MeOH to each sample and then cells were frozen at -80 ºC until metabolomics and lipidomic analysis.

Sample Preparation:

Sampleprep ID:SP003259
Sampleprep Summary:Frozen cells in MeOH were thawed at 4˚C. Then a first extraction targeted at lipid metabolites was performed by adding MTBE to a final concentration of MTBE: MeOH (1:4). Samples were then sonicated for a total of 15 min at 15W (3 rounds of 5 min sonication), thoroughly vortexed, and centrifuged for 10 min at 16000 g to remove any debris. The supernatant was collected. Then a second extraction took place to obtain the most polar metabolites in the sample. To that extent, 100 μl of a mixture of H2O:MeOH (1:4) was added and the sample was sonicated again for a total of 15 min at 15W (3 rounds of 5 min sonication), thoroughly vortexed and centrifuged for 10 min at 16000 g to remove any debris. The supernatant was collected. Polar samples were kept at 4 degrees until their analysis. Extraction solvents were used as a blank and followed the same procedure as the samples. Quality control (QC) samples were prepared by pooling equal volumes of samples from the same cell type separately. Additionally, to select features produced only by cells, a calibration curve was made of Teff or Treg cells, respectively. Samples were divided into 2 groups depending on the type of subpopulation they belong to either Teff or Treg, and randomized.
Extract Storage:-80℃

Chromatography:

Chromatography ID:CH003895
Chromatography Summary:For polar metabolites separation, 2 μL of the sample were injected into a Zorbax Extend C18 (4.6 × 50 mm, 1.8 μm; Agilent, Waldbronn, Germany), with a guard column Zorbax Extend C18 (3 × 5 mm, 1.8 μm; Agilent), both maintained at 60 °C. The flow rate was set at 0.6 mL/min. The elution gradient involved a mobile phase consisting of: (A) water containing 0.1% of formic acid and (B) acetonitrile containing 0.1% of formic acid. The initial conditions were set at 5% phase B for 1 min, which increased linearly to 80% phase B in 7 min. Then in 4.5 min it increased until 100% of phase. Then the equipment returned to the initial conditions in 0.5 min, which were held for 3 min for column reconditioning.
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent ZORBAX RRHD Extend-C18 (50 x 2.1mm,1.8um)
Column Temperature:60 ºC
Flow Gradient:0-1 min: 5% B; 1-8 min: linear increase until 80% B; 8-12.5 min: linear increase until 100% B. Then the equipment returned to the initial conditions in 0.5 min, which were held for 3 min for column reconditioning.
Flow Rate:0.6 mL/min
Solvent A:100% water; 0.1% of formic acid
Solvent B:100% acetonitrile; 0.1% of formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003896
Chromatography Summary:For the lipidic extraction, the Agilent 1290 Infinity II Multisampler system, equipped with a multi-wash option, was used to uptake 1 and 2 µL of extracted samples in positive and negative ionization modes, respectively. The multisampler temperature was maintained at 15 °C to preserve lipids in a stable environment and avoid precipitation. An Agilent InfinityLab Poroshell 120 ECsingle bondC18 (3.0 × 100 mm, 2.7 µm) (Agilent Technologies) column and a compatible guard column (Agilent InfinityLab Poroshell 120 ECsingle bondC18, 3.0 × 5 mm, 2.7 µm) were used and maintained at 50 °C. The chromatography gradient started at 70% of B at 0 – 1 min, 86% at 3.5 – 10 min, 100% B at 11–17 min. The starting conditions were recovered by minute 17, followed by a 2 min re-equilibration time; the total running time was 19 min. The mobile phases used for both positive and negative ionization modes consisted of (A) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in 9:1 water/methanol and (B) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in 2:3:5 acetonitrile/methanol/isopropanol. The flow rate was held constant, set at 0.6 mL/min. The multi-wash strategy consisted of a mixture of methanol:isopropanol (50:50, v/v) with the wash time set at 15 s, and aqueous phase:organic phase (30:70, v/v) mixture to assist in the starting conditions.
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:50 ºC
Flow Gradient:0-1 min: 70% B; 1-3.5 min: linear increase until 86% B; 3.5-10 min: 86% B; 10-11 min: linear increase until 100% B; 11-17 min: 100% B. Then the equipment returned to the initial conditions in 0.1 min, which were held for 1.9 min for column reconditioning.
Flow Rate:0.6 mL/min
Solvent A:water/methanol (9/1); 10 mM ammonium acetate; 0.2 mM ammonium fluoride
Solvent B:acetonitrile/methanol/isopropanol (2/3/5); 10 mM ammonium acetate; 0.2 mM ammonium fluoride
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005145
Laboratory Name:Centre of Metabolomics and Bioanalysis (CEMBIO)
Analysis Type:MS
Chromatography ID:CH003895
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003135_AN005145_Results.txt
Units:Peak area
  
Analysis ID:AN005146
Laboratory Name:Centre of Metabolomics and Bioanalysis (CEMBIO)
Analysis Type:MS
Chromatography ID:CH003895
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003135_AN005146_Results.txt
Units:Peak area
  
Analysis ID:AN005147
Laboratory Name:Centre of Metabolomics and Bioanalysis (CEMBIO)
Analysis Type:MS
Chromatography ID:CH003896
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003135_AN005147_Results.txt
Units:Peak area
  
Analysis ID:AN005148
Laboratory Name:Centre of Metabolomics and Bioanalysis (CEMBIO)
Analysis Type:MS
Chromatography ID:CH003896
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003135_AN005148_Results.txt
Units:Peak area
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