Summary of Study ST002988
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 PR001831. The data can be accessed directly via it's Project DOI: 10.21228/M81Q73 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.
| Study ID | ST002988 |
| Study Title | Polar urinary metabolomics of a patient cohort |
| Study Type | (un)targeted MS |
| Study Summary | This study is part of a multi-part study, including a. longitudinal polar fecal metabolomics of mice undergoing sensitization to beta-lactoglobulin b. polar fecal metabolomics of a patient cohort c. fecal lipidomics of a patient cohort d. polar urinary metabolomics of a patient cohort e. polar metabolomics of in vitro digestions This specific part is part d. polar urinary metabolomics of a patient cohort |
| Institute | Ghent University |
| Department | Department of Translational Physiology, Infectiology and Public Health |
| Laboratory | Laboratory for Integrative Metabolomics |
| Last Name | De Paepe |
| First Name | Ellen |
| Address | Salisburylaan 133, 9820 Merelbeke, Belgium |
| Ellen.DePaepe@UGent.be | |
| Phone | 0032479081098 |
| Submit Date | 2023-07-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001831 |
| Project DOI: | doi: 10.21228/M81Q73 |
| Project Title: | Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow’s milk allergy |
| Project Type: | (un)targeted MS |
| Project Summary: | Background: IgE-mediated cow’s milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies. Methods: We report a longitudinal in vivo murine model, in which 2 mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n=6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-γ) measured, and fecal samples subjected to metabolomics. The results of the murine models were further supported by fecal microbiome-metabolome data from our population of IgE-CMA (n=24) and healthy (n=23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes. Results: During sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. The latter was reflected in a disturbed sphingolipid metabolism. We confirmed microbial dysbiosis, and its causal effect on metabolic alterations in our patient cohort, which was accompanied by metabolic signatures of low-grade inflammation. Conclusion: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies. |
| Institute: | Ghent University |
| Department: | Translational Physiology, Infectiology and Public Health |
| Laboratory: | Laboratory for Integrative Metabolomics |
| Last Name: | De Paepe |
| First Name: | Ellen |
| Address: | Salisburylaan 133, Merelbeke, Oost-Vlaanderen, 9820, Belgium |
| Email: | Ellen.DePaepe@UGent.be |
| Phone: | 0032479081098 |
| Funding Source: | Fonds Wetenschappelijk Onderzoek |
Subject:
| Subject ID: | SU003101 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | < 5 years old |
| Gender: | Male and female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | IgE CMA |
|---|---|---|
| SA325660 | iQC15 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325661 | iQC16 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325662 | iQC2 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325663 | iQC14 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325664 | iQC12 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325665 | iQC10 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325666 | iQC11 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325667 | iQC3 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325668 | iQC13 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325669 | iQC1 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325670 | iQC4 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325671 | iQC9 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325672 | iQC7 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325673 | iQC8 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325674 | iQC6 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325675 | iQC5 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325676 | 81 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325677 | 43 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325678 | 40 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325679 | 45 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325680 | 104 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325681 | 54 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325682 | 65 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325683 | 68 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325684 | 108 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325685 | 51 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325686 | 49 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325687 | 112 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325688 | 3 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325689 | 109 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325690 | 27 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325691 | 4 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325692 | 22 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325693 | 130 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325694 | 60 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325695 | 116 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325696 | 113 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA325697 | 78 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325698 | 92 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325699 | 79 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325700 | 123 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325701 | 80 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325702 | 127 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325703 | 64 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325704 | 31 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325705 | 25 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325706 | 42 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325707 | 35 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325708 | 39 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325709 | 37 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325710 | 41 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325711 | 20 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325712 | 10 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325713 | 14 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325714 | 7 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA325715 | 5 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325716 | 8 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325717 | 1 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325718 | 12 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325719 | 32 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325720 | 115 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325721 | 44 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325722 | 73 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325723 | 52 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325724 | 58 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325725 | 70 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325726 | 96 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325727 | 34 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA325728 | 18 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA325729 | 6 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA325730 | 97 | 0 | IgE other:2 | non-IgE CMA:0 | Healthy:0 |
| SA325731 | 99 | 0 | IgE other:2 | non-IgE CMA:0 | Healthy:0 |
| SA325732 | 24 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325733 | 57 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325734 | 2 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325735 | 53 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325736 | 26 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325737 | 84 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325738 | 85 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325739 | 86 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325740 | 36 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325741 | 30 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325742 | 128 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325743 | 136 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325744 | 29 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA325745 | 21 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325746 | 59 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325747 | 95 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325748 | 28 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA325749 | 16 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| Showing results 1 to 90 of 90 |
Collection:
| Collection ID: | CO003094 |
| Collection Summary: | Urine samples were collected using The Newcastle Urine Collector (SteriSets Medical Products, Guilhufe, Portugal) or directly in a plastic container. Samples were stored at -20 °C until pick-up (< 1 week). Following cooled transport (dry ice or icepacks). Urine samples were thawed and aliquoted upon arrival and stored at -80 °C awaiting analysis. |
| Sample Type: | Urine |
| Collection Method: | Spontaneous defecation |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003110 |
| Treatment Summary: | No treatment was applied, patients were divided into 4 different control groups: - IgE-mediated cow's milk allergy - other functional gastrointestinal disorder - IgE-mediated other food allergy - healthy brothers and sisters |
Sample Preparation:
| Sampleprep ID: | SP003107 |
| Sampleprep Summary: | Extraction of the urinary metabolome was initiated by pipetting 300 mL urine into a 1.5-mL Eppendorf tube, after which 30 mL of ISTD mixture (100 ng mL&1 D-valine-d8 and of L-alanine-d3) was added. Following this, the sample was centrifuged for 8 min (1 000 x g, 4 %C). Next, 100 mL supernatant was collected and diluted (1:10) with ultrapure water, after which the resulting extract was transferred to a glass HPLC-vial. |
| Processing Storage Conditions: | -80℃ |
| Sample Spiking: | Internal standard |
Combined analysis:
| Analysis ID | AN004908 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | a.u. |
Chromatography:
| Chromatography ID: | CH003703 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 45 |
| Flow Gradient: | A gradient profile with following proportions (v/v) of solvent A was applied: 0-1.5 min at 98%, 1.5-7.0 min from 98% to 75%, 7.0-8.0 min from 75% to 40%, 8.0-12.0 min from 40% to 5%, 12.0-14.0 min at 5%, 14.0-14.1 min from 5 to 98%, followed by 4.0 min of re-equilibration. |
| Flow Rate: | 0.4 mL/min |
| Internal Standard: | L-alanine-d3, D-valine-d8 |
| Sample Injection: | 10 uL |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004651 |
| Analysis ID: | AN004908 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS acquisition: Xcalibur Targeted data processing: Xcalibur Untargeted data acquisition: Compound Discoverer, R studio Ion mode is unspecified as analysis is performed in polarity switching mode, thereby generating data for both positive and negative ionization at the same time. |
| Ion Mode: | UNSPECIFIED |
