Summary of Study ST002438

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 PR001570. The data can be accessed directly via it's Project DOI: 10.21228/M8RM66 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 IDST002438
Study TitleOzone alters glycosphingolipid metabolism and exacerbates characteristics of asthma in mice
Study SummaryAsthma is a common chronic respiratory disease exacerbated by multiple environmental factors, including exposure to air pollutants such as ozone. Acute ozone exposure has previously been implicated in airway inflammation, airway hyperreactivity, and other characteristics of asthma. Altered sphingolipid metabolism following ozone exposure may contribute to the molecular mechanisms underlying these previously reported effects. This study aimed to identify changes in metabolomic profiles and characteristics of asthma in allergen-sensitized mice following ozone exposure to provide insights regarding mechanisms of ozone-induced exacerbations in asthma. Adult male and female BALB/c mice were sensitized intranasally to house dust mite allergen (HDM) on days 1, 3, and 5 followed by HDM challenge on days 12-14. Mice were subsequently exposed to ozone following each HDM challenge for 6 hr/day. Bronchoalveolar lavage, plasma, whole lung lobes, and microdissected lung airways were collected from 8 female and 8 male mice for metabolomics analysis. 6 female and 6 male mice underwent methacholine challenge using a forced oscillation technique to assess pulmonary function. HDM-sensitized male mice exposed to ozone displayed synergistically increased airway hyperreactivity as well as increased airway inflammation and eosinophilia relative to control mice. Effects in male mice were significantly more severe than the effects observed in females. Both HDM-sensitized male and female mice exposed to ozone displayed significant decreases in multiple classes of sphingolipids in microdissected airways. However, glycosphingolipids were significantly increased in females and to a lesser extent in males. These results potentially implicate glycosphingolipids in protecting against severe outcomes of ozone exposure that coincide with exacerbation of allergic asthma.
Institute
University of California, Davis
Last NameStevens
First NameNathanial
Address451 Health Sciences Drive
Emailncstevens@ucdavis.edu
Phone8282844315
Submit Date2022-08-25
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-01-25
Release Version1
Nathanial Stevens Nathanial Stevens
https://dx.doi.org/10.21228/M8RM66
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001570
Project DOI:doi: 10.21228/M8RM66
Project Title:Ozone alters glycosphingolipid metabolism and exacerbates characteristics of asthma in mice
Project Summary:Asthma is a common chronic respiratory disease exacerbated by multiple environmental factors, including exposure to air pollutants such as ozone. Acute ozone exposure has previously been implicated in airway inflammation, airway hyperreactivity, and other characteristics of asthma. Altered sphingolipid metabolism following ozone exposure may contribute to the molecular mechanisms underlying these previously reported effects. This study aimed to identify changes in metabolomic profiles and characteristics of asthma in allergen-sensitized mice following ozone exposure to provide insights regarding mechanisms of ozone-induced exacerbations in asthma. Adult male and female BALB/c mice were sensitized intranasally to house dust mite allergen (HDM) on days 1, 3, and 5 followed by HDM challenge on days 12-14. Mice were subsequently exposed to ozone following each HDM challenge for 6 hr/day. Bronchoalveolar lavage, plasma, whole lung lobes, and microdissected lung airways were collected from 8 female and 8 male mice for metabolomics analysis. 6 female and 6 male mice underwent methacholine challenge using a forced oscillation technique to assess pulmonary function. HDM-sensitized male mice exposed to ozone displayed synergistically increased airway hyperreactivity as well as increased airway inflammation and eosinophilia relative to control mice. Effects in male mice were significantly more severe than the effects observed in females. Both HDM-sensitized male and female mice exposed to ozone displayed significant decreases in multiple classes of sphingolipids in microdissected airways. However, glycosphingolipids were significantly increased in females and to a lesser extent in males. These results potentially implicate glycosphingolipids in protecting against severe outcomes of ozone exposure that coincide with exacerbation of allergic asthma.
Institute:University of California Davis
Last Name:Stevens
First Name:Nathanial
Address:451 Health Sciences Drive, Davis, CA, 95616, USA
Email:ncstevens@ucdavis.edu
Phone:8282844315
Funding Source:R21 ES030276, T32 ES007059, T32 HL007013, NIH U19 AG023122

Subject:

Subject ID:SU002527
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:BALB/c
Age Or Age Range:8-10 wks.
Gender:Male and female
Animal Animal Supplier:Envigo
Animal Light Cycle:12/12 light/dark

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA243615mx626289_OzAW_BR3BR
SA243616mx626289_OzAW_BR1BR
SA243617mx626289_OzAW_BR4BR
SA243618mx626289_OzAW_BR2BR
SA243619mx626289_OzAW_BR7BR
SA243620mx626289_OzAW_BR6BR
SA243621mx626289_OzAW_BR5BR
SA243622mx626289_OzAW_75HFA_F
SA243623mx626289_OzAW_74HFA_F
SA243624mx626289_OzAW_76HFA_F
SA243625mx626289_OzAW_80HFA_F
SA243626mx626289_OzAW_73HFA_F
SA243627mx626289_OzAW_79HFA_F
SA243628mx626289_OzAW_78HFA_F
SA243629mx626289_OzAW_77HFA_F
SA243630mx626289_OzAW_65HFA_M
SA243631mx626289_OzAW_70HFA_M
SA243632mx626289_OzAW_71HFA_M
SA243633mx626289_OzAW_66HFA_M
SA243634mx626289_OzAW_67HFA_M
SA243635mx626289_OzAW_69HFA_M
SA243636mx626289_OzAW_68HFA_M
SA243637mx626289_OzAW_72HFA_M
SA243638mx626289_OzAW_89HO3_F
SA243639mx626289_OzAW_94HO3_F
SA243640mx626289_OzAW_95HO3_F
SA243641mx626289_OzAW_96HO3_F
SA243642mx626289_OzAW_93HO3_F
SA243643mx626289_OzAW_92HO3_F
SA243644mx626289_OzAW_90HO3_F
SA243645mx626289_OzAW_91HO3_F
SA243646mx626289_OzAW_83HO3_M
SA243647mx626289_OzAW_82HO3_M
SA243648mx626289_OzAW_86HO3_M
SA243649mx626289_OzAW_88HO3_M
SA243650mx626289_OzAW_87HO3_M
SA243651mx626289_OzAW_81HO3_M
SA243652mx626289_OzAW_85HO3_M
SA243653mx626289_OzAW_84HO3_M
SA243654mx626289_OzAW_MB06MB
SA243655mx626289_OzAW_MB07MB
SA243656mx626289_OzAW_MB05MB
SA243657mx626289_OzAW_MB04MB
SA243658mx626289_OzAW_MB01MB
SA243659mx626289_OzAW_MB02MB
SA243660mx626289_OzAW_MB03MB
SA243661mx626289_OzAW_P1P
SA243662mx626289_OzAW_P3P
SA243663mx626289_OzAW_P2P
SA243664mx626289_OzAW_P5P
SA243665mx626289_OzAW_P7P
SA243666mx626289_OzAW_P4P
SA243667mx626289_OzAW_P6P
SA243668mx626289_OzAW_16SFA_F
SA243669mx626289_OzAW_11SFA_F
SA243670mx626289_OzAW_10SFA_F
SA243671mx626289_OzAW_15SFA_F
SA243672mx626289_OzAW_14SFA_F
SA243673mx626289_OzAW_12SFA_F
SA243674mx626289_OzAW_9SFA_F
SA243675mx626289_OzAW_13SFA_F
SA243676mx626289_OzAW_1SFA_M
SA243677mx626289_OzAW_6SFA_M
SA243678mx626289_OzAW_5SFA_M
SA243679mx626289_OzAW_4SFA_M
SA243680mx626289_OzAW_3SFA_M
SA243681mx626289_OzAW_7SFA_M
SA243682mx626289_OzAW_8SFA_M
SA243683mx626289_OzAW_2SFA_M
SA243684mx626289_OzAW_26SO3_F
SA243685mx626289_OzAW_29SO3_F
SA243686mx626289_OzAW_30SO3_F
SA243687mx626289_OzAW_32SO3_F
SA243688mx626289_OzAW_28SO3_F
SA243689mx626289_OzAW_31SO3_F
SA243690mx626289_OzAW_25SO3_F
SA243691mx626289_OzAW_27SO3_F
SA243692mx626289_OzAW_18SO3_M
SA243693mx626289_OzAW_19SO3_M
SA243694mx626289_OzAW_20SO3_M
SA243695mx626289_OzAW_22SO3_M
SA243696mx626289_OzAW_24SO3_M
SA243697mx626289_OzAW_21SO3_M
SA243698mx626289_OzAW_17SO3_M
SA243699mx626289_OzAW_23SO3_M
Showing results 1 to 85 of 85

Collection:

Collection ID:CO002520
Collection Summary:Right lung lobes were microdissected following a previous protocol (Plopper et al. 1991; Stevens et al. 2021). Briefly, 3 right lobes from each mouse collected during necropsy were blunt dissected on ice by removal of the surrounding lung parenchyma from the airways. The dissected lung airways were promptly transferred and stored at -80 degrees C until preparation for metabolomics analysis.
Sample Type:Lung airways

Treatment:

Treatment ID:TR002539
Treatment Summary:Mice underwent intranasal instillation with either house-dust mite dissolved in PBS or vehicle on days 1,3, and 5. Mice were challenged with HDM or vehicle on days 12-14 and subsequently exposed to either filtered air or ozone (0.5ppm, 6hr./day) after each challenge.

Sample Preparation:

Sampleprep ID:SP002533
Sampleprep Summary:Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Combined analysis:

Analysis ID AN003972 AN003973 AN003974 AN003975
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish Agilent 6490 Agilent 6490
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Agilent HP5-MS (30m x 0.25mm, 0.25 um) Agilent HP5-MS (30m x 0.25mm, 0.25 um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Relative abundance Relative abundance Relative abundance Relative abundance

Chromatography:

Chromatography ID:CH002937
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002938
Instrument Name:Agilent 6490
Column Name:Agilent HP5-MS (30m x 0.25mm, 0.25 um)
Chromatography Type:HILIC

MS:

MS ID:MS003706
Analysis ID:AN003972
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions.
Ion Mode:POSITIVE
  
MS ID:MS003707
Analysis ID:AN003973
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions.
Ion Mode:NEGATIVE
  
MS ID:MS003708
Analysis ID:AN003974
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions.
Ion Mode:POSITIVE
  
MS ID:MS003709
Analysis ID:AN003975
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions.
Ion Mode:NEGATIVE
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