Summary of Study ST002230
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 PR001420. The data can be accessed directly via it's Project DOI: 10.21228/M85M5J 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 | ST002230 |
| Study Title | Metabolomics of bone marrow-derived dendritic cells conditioned with H. polygyrus bakery non-polar metabolites |
| Study Summary | Bone marrow-derived dendritic cells were incubated with 50 micro g/mL of H. polygyrus bakery non-polar metabolites in RPMI 1640 containing 10% FBS, 1% of 100X penicillin/streptomycin, 1% of 100 mM sodium pyruvate, and 20 ng/mL GM-CSF at 37°C, 5% CO2 for 4 or 20 h. Supernatants and cell-free media controls were collected and incubated with ice-cold HPLC-grade methanol for 30 min on ice, centrifuged at 10,000 x g for 10 min at 4°C and stored at -80°C until analysis. The profiling of nonpolar metabolites was performed by LC-MS/MS analysis of the deproteinated conditioned media by injecting 3 mL of sample onto a Dionex UHPLC system equipped with an Agilent Eclipse C18 (2.1 x 15 mm, 1.8 mm) column incubated at 45oC. Metabolites were resolved with a 30 min linear running 0-80 % using the buffers system 0.05 % formic acid and 0.05 % formic acid in acetonitrile at a flowrate of 300 mL/min. The column effluent was introduced by electrospray ionization onto a ThermoScientific Velos LTQ Orbitrap Analyzer using a spray voltage of 3.6 kV, a source heater temperature of 350oC, and a sheath gas flow of 40 L/min. Survey scans were performed using the Orbitrap mass spectrometer and the 10 most intense ions were selected for fragmentation using a 30-40 V stepped collision induced dissociation energy. Fragmentation products were analyzed in the linear ion trap mass spectrometer. Fragmentation was used to perform XCMS online database (https://xcmsonline.scripps.edu) search to identify possible metabolites. |
| Institute | McGill University |
| Last Name | Lopes |
| First Name | Fernando |
| Address | 21111 Lakeshore Rd |
| fernando.lopes@mcgill.ca | |
| Phone | 5143987607 |
| Submit Date | 2022-07-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-07-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001420 |
| Project DOI: | doi: 10.21228/M85M5J |
| Project Title: | Metabolomics of bone marrow-derived dendritic cells conditioned with H. polygyrus bakery non-polar metabolites |
| Project Summary: | Aim: Characterize tolerogenic responses induced by helminth-derived metabolites (HDM) in dendritic cells (DCs). Methods: H. polygyrus worms were culture for 24h and HDMs were isolated from conditioned media by chromatography. Bone marrow-derived dendritic cells (BMDCs) were treated with HDM for 4 or 20 h. Cells were either stimulated with LPS or adoptively transferred to mice. Cytokine secretion was measured by ELISA. The metabolome of HDM-treated DCs were assessed by mass spectrometry, respectively. Results: Pre-treatment with HDM decreased LPS-induced TNF and increased IL-10 release by BMDCs. Importantly, HDM decreased expression of MHC-II, CD86, and CD40 in BMDCs and splenic DCs, suggesting that HDM induces a tolerogenic profile on DCs. The metabolomic approach revealed a total of 17 downregulated metabolites, against one upregulated of the 225 total peaks analyzed. Functional analyses were performed and results predicted a total of 29 pathways and 43 matched compounds. Scatter plot test of significant peaks revealed two differentially enriched pathways, the sphingolipid metabolism, and a highly enriched pathway, the terpenoid backbone metabolism, witch C00418 metabolite is a potential match to mevalonic acid, according to KEGG compound database in HDM-treated DCs in comparison with naïve DCs. These differentially expressed genes and enriched metabolites may indicate a novel mechanism by which helminths induce a tolerogenic profile in DCs. |
| Institute: | McGill University |
| Last Name: | Lopes |
| First Name: | Fernando |
| Address: | 21111 Lakeshore Rd |
| Email: | fernando.lopes@mcgill.ca |
| Phone: | 5143987607 |
Subject:
| Subject ID: | SU002316 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Experimental variables |
|---|---|---|
| SA212554 | FLmedia_1 | Cell-free media |
| SA212555 | FLmedia_3 | Cell-free media |
| SA212556 | FLmedia_2 | Cell-free media |
| SA212557 | FLcontrol20h_4 | Supernatant of DCs negative control cultured for 20h |
| SA212558 | FLcontrol20h_1 | Supernatant of DCs negative control cultured for 20h |
| SA212559 | FLcontrol20h_2 | Supernatant of DCs negative control cultured for 20h |
| SA212560 | FLcontrol20h_3 | Supernatant of DCs negative control cultured for 20h |
| SA212561 | FLControl4h_3 | Supernatant of DCs negative control cultured for 4h |
| SA212562 | FLControl4h_2 | Supernatant of DCs negative control cultured for 4h |
| SA212563 | FLControl4h_1 | Supernatant of DCs negative control cultured for 4h |
| SA212564 | FLHpb20h_3 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 20h |
| SA212565 | FLHpb20h_4 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 20h |
| SA212566 | FLHpb20h_2 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 20h |
| SA212567 | FLHpb20h_1 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 20h |
| SA212568 | Hpb4h_4 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 4h |
| SA212569 | Hpb4h_2 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 4h |
| SA212570 | Hpb4h_1 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 4h |
| SA212571 | Hpb4h_3 | Supernatant of DCs treated with H. polygyrus bakery non-polar metabolites for 4h |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002309 |
| Collection Summary: | Bone marrow-derived dendritic cells were incubated with 50 micro g/mL of H. polygyrus bakery non-polar metabolites in RPMI 1640 containing 10% FBS, 1% of 100X penicillin/streptomycin, 1% of 100 mM sodium pyruvate, and 20 ng/mL GM-CSF at 37°C, 5% CO2 for 4 or 20 h. Supernatants and cell-free media controls were collected and incubated with ice-cold HPLC-grade methanol for 30 min on ice, centrifuged at 10,000 x g for 10 min at 4°C and stored at -80°C until analysis. |
| Collection Protocol Filename: | Summary_of_the_study_protocols.docx |
| Sample Type: | Dendritic cells |
Treatment:
| Treatment ID: | TR002328 |
| Treatment Summary: | Bone marrow-derived dendritic cells were incubated with 50 micro g/mL of H. polygyrus bakery non-polar metabolites in RPMI 1640 containing 10% FBS, 1% of 100X penicillin/streptomycin, 1% of 100 mM sodium pyruvate, and 20 ng/mL GM-CSF at 37°C, 5% CO2 for 4 or 20 h. Supernatants and cell-free media controls were collected and incubated with ice-cold HPLC-grade methanol for 30 min on ice, centrifuged at 10,000 x g for 10 min at 4°C and stored at -80°C until analysis. |
Sample Preparation:
| Sampleprep ID: | SP002322 |
| Sampleprep Summary: | Bone marrow-derived dendritic cells were incubated with 50 micro g/mL of H. polygyrus bakery non-polar metabolites in RPMI 1640 containing 10% FBS, 1% of 100X penicillin/streptomycin, 1% of 100 mM sodium pyruvate, and 20 ng/mL GM-CSF at 37°C, 5% CO2 for 4 or 20 h. Supernatants and cell-free media controls were collected and incubated with ice-cold HPLC-grade methanol for 30 min on ice, centrifuged at 10,000 x g for 10 min at 4°C and stored at -80°C until analysis. |
| Sampleprep Protocol Filename: | Summary_of_the_study_protocols.docx |
Chromatography:
| Chromatography ID: | CH002694 |
| Methods Filename: | Summary_of_the_study_protocols.docx |
| Instrument Name: | Thermo Dionex |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN003639 |
| Analysis Type: | MS |
| Analysis Protocol File: | Summary_of_the_study_protocols.docx |
| Chromatography ID: | CH002694 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST002230_AN003639_Results.txt |
| Units: | M/z |
