Summary of Study ST003133
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 PR001946. The data can be accessed directly via it's Project DOI: 10.21228/M85X5N 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 | ST003133 |
| Study Title | Unraveling Salivary Metabolome in Children with Eosinophilic Esophagitis |
| Study Type | untargeted metabolomics analysis |
| Study Summary | In this pilot study, we performed global untargeted salivary metabolomics. We focused on salivary metabolomics as oral mucosa is the initial interface between the triggering antigens and the host mucosal immune system,9 saliva is rich yet understudied biofluid, and saliva can be collected safely, rapidly, and non-invasively (compared to esophageal and plasma samples) making it uniquely suited for testing pediatric populations.10 Our primary aim was to gain novel insights into the upstream metabolomic alterations in pediatric EoE by profiling salivary metabolome in children with EoE, and our secondary aim was to assess the translational potential of salivary metabolites. |
| Institute | Vanderbilt University |
| Department | Chemistry |
| Laboratory | Center for Innovative Technology |
| Last Name | CODREANU |
| First Name | SIMONA |
| Address | 1234 STEVENSON CENTER LANE |
| SIMONA.CODREANU@VANDERBILT.EDU | |
| Phone | 6158758422 |
| Submit Date | 2024-03-20 |
| Num Groups | 4 |
| Total Subjects | 28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001946 |
| Project DOI: | doi: 10.21228/M85X5N |
| Project Title: | Unraveling Salivary Metabolome in Children with Eosinophilic Esophagitis: Insights into Disease Pathogenesis and Translational Potential. |
| Project Summary: | In this pilot study, we performed global untargeted salivary metabolomics. We focused on salivary metabolomics as oral mucosa is the initial interface between the triggering antigens and the host mucosal immune system,9 saliva is rich yet understudied biofluid, and saliva can be collected safely, rapidly, and non-invasively (compared to esophageal and plasma samples) making it uniquely suited for testing pediatric populations.10 Our primary aim was to gain novel insights into the upstream metabolomic alterations in pediatric EoE by profiling salivary metabolome in children with EoE, and our secondary aim was to assess the translational potential of salivary metabolites. |
| Institute: | Vanderbilt University |
| Department: | Chemistry |
| Laboratory: | Center for Innovative Technology |
| Last Name: | CODREANU |
| First Name: | SIMONA |
| Address: | 1234 STEVENSON CENTER LANE |
| Email: | SIMONA.CODREANU@VANDERBILT.EDU |
| Phone: | 6158758422 |
Subject:
| Subject ID: | SU003250 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | Eosinophilic esophagitis EoE |
| Age Or Age Range: | children (6-18 years) |
| Gender: | Male and female |
| Human Inclusion Criteria: | Children diagnosed with EoE or with symptoms suggestive of EoE and undergoing EGD with biopsies for clinical care were consecutively enrolled |
| Human Exclusion Criteria: | Children with inflammatory bowel disease, celiac disease, connective tissue disorder, prior esophageal injury or surgery, esophageal varices, use of systemic steroids or antibiotics within the previous 30 days, neurodevelopmental delays, or with a visible oral ulcer or gingival disease were excluded. |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA339302 | A4 | saliva | Active EoE |
| SA339303 | A3 | saliva | Active EoE |
| SA339304 | A2 | saliva | Active EoE |
| SA339305 | A5 | saliva | Active EoE |
| SA339306 | A7 | saliva | Active EoE |
| SA339307 | A9 | saliva | Active EoE |
| SA339308 | A8 | saliva | Active EoE |
| SA339309 | A1 | saliva | Active EoE |
| SA339310 | A6 | saliva | Active EoE |
| SA339311 | In6 | saliva | Inactive EoE |
| SA339312 | In5 | saliva | Inactive EoE |
| SA339313 | In4 | saliva | Inactive EoE |
| SA339314 | In7 | saliva | Inactive EoE |
| SA339315 | In8 | saliva | Inactive EoE |
| SA339316 | In10 | saliva | Inactive EoE |
| SA339317 | In9 | saliva | Inactive EoE |
| SA339318 | In3 | saliva | Inactive EoE |
| SA339319 | In2 | saliva | Inactive EoE |
| SA339320 | In1 | saliva | Inactive EoE |
| SA339321 | N2 | saliva | negative control-GERD |
| SA339322 | N1 | saliva | negative control-GERD |
| SA339323 | N5 | saliva | negative control-GERD |
| SA339324 | N3 | saliva | negative control-GERD |
| SA339325 | N4 | saliva | negative control-GERD |
| SA339326 | P4 | saliva | positive control- nonEoE |
| SA339327 | P1 | saliva | positive control- nonEoE |
| SA339328 | P5 | saliva | positive control- nonEoE |
| SA339329 | P2 | saliva | positive control- nonEoE |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO003243 |
| Collection Summary: | Saliva samples were collected immediately before the scheduled EGD. All participants were nil per os for at least 6 hours before the procedure, and the saliva samples were collected in a sterile tube (BD Biosciences, San Jose, CA) between 7:30 am and 11:30 am. After collection, the samples were maintained at 4°C and transported to the laboratory within 2 hours. In the laboratory, the saliva samples were centrifuged at 3000 rpm for 15 mins at room temperature to remove particulate debris, and the supernatant was stored in aliquots at -80°C until analysis. |
| Collection Protocol Filename: | Sample_collection.pdf |
| Sample Type: | Saliva |
| Storage Conditions: | -80℃ |
| Collection Vials: | sterile tube (BD Biosciences, San Jose, CA) |
| Collection Tube Temp: | 4 |
Treatment:
| Treatment ID: | TR003259 |
| Treatment Summary: | After collection, the samples were maintained at 4°c C and transported to the laboratory within 2 hours. In the laboratory, the saliva samples were centrifuged at 3000 rpm for 15 mins at room temperature to remove particulate debris, and the supernatant was stored in aliquots at -80°C until analysis. |
| Treatment Protocol Filename: | Sample_collection.pdf |
Sample Preparation:
| Sampleprep ID: | SP003257 |
| Sampleprep Summary: | Briefly, after thawing, the samples were normalized by total protein amount (50 µg) following a Bicinchoninic acid assay (Thermo Fisher Scientific, Waltham, MA). Metabolites were extracted using an ice-cold solvent of methanol/water (80:20, v/v) mixture. Heavy-labeled phenylalanine-D8 and biotin-D2 was were added to individual samples before protein precipitation to be able to assess sample preparation reproducibility. Following overnight incubation at -80°C, precipitated proteins were pelleted by centrifugation at 10,000 rpm for 10 min, and metabolite extracts were then dried in vacuo and stored at -80°C. Individual extracts were reconstituted in 100 µl of acetonitrile/water (80:20, v/v) containing heavy-labeled carnitine-D9, tryptophan-D3, valine-D8, and inosine-4N15, and centrifuged for 5 min at 10,000 rpm to remove insoluble material. A pooled quality control sample (QC) was prepared by pooling equal volumes of individual samples. |
| Sampleprep Protocol Filename: | MS_Methods.pdf |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Following standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum. |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN005143 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak intensity |
Chromatography:
| Chromatography ID: | CH003893 |
| 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; 95%A, 5%B |
| Flow Rate: | 0.20mL/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:
| MS ID: | MS004879 |
| Analysis ID: | AN005143 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The full mass scan was acquired at 120,000 resolutions with a scan rate of 3.5 Hz and an automatic gain control (AGC) target of 1x106. A maximum ion injection time of 100 ms and MS/MS spectra were collected at 15,000 resolutions, with an AGC target of 2x105 ions and a maximum ion injection time of 100 ms All mass spectrometry data was imported, processed, normalized, and reviewed using Progenesis QI v.3.0 (Non-linear Dynamics, Newcastle, UK) |
| Ion Mode: | POSITIVE |
