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.

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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
Email	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

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

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.

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

Combined analysis:

Analysis ID	AN003639
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Dionex
Column	Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo LTQ Discovery Orbitrap
Ion Mode	POSITIVE
Units	M/z

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

MS:

MS ID:	MS003390
Analysis ID:	AN003639
Instrument Name:	Thermo LTQ Discovery Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	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.
Ion Mode:	POSITIVE
Analysis Protocol File:	Summary_of_the_study_protocols.docx