Summary of study ST001312

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 PR000890. The data can be accessed directly via it's Project DOI: 10.21228/M8ND7K This work is supported by NIH grant, U2C- DK119886.

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Study IDST001312
Study TitleLipid expression in serum after early lifer exposure to an endocrine disruptor at 70 days postnatal (part-III)
Study TypeLipid expression after chemical exposure versus control.
Study SummaryOur early-life environment has a profound influence on developing organs that impact metabolic function and determines disease susceptibility across the life-course. Using a rat model for exposure to an endocrine disrupting chemical (EDC), we show that early-life exposure causes metabolic dysfunction in adulthood and reprograms histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature. This epigenomic reprogramming persists long after the initial exposure, but many reprogrammed genes remain transcriptionally silent with their impact on metabolism not revealed until a later life exposure to a Western-style diet. Diet-dependent metabolic disruption was largely driven by reprogramming of the Early Growth Response 1 (EGR1) transcriptome and production of metabolites in pathways linked to cholesterol, lipid and one-carbon metabolism. These findings demonstrate the importance of epigenome:environment interactions, which early in life accelerate epigenomic aging, and later in adulthood unlock metabolically restricted epigenetic reprogramming to drive metabolic dysfunction.
Institute
Baylor College of Medicine
Last NameWalker
First NameCheryl
Address1 Baylor Plaza
EmailCheryl.walker@bcm.edu
Phone7137988219
Submit Date2020-01-24
Num Groups2
Total Subjects10
Num Males10
Analysis Type DetailLC-MS
Release Date2020-03-11
Release Version1
Cheryl Walker Cheryl Walker
https://dx.doi.org/10.21228/M8ND7K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000890
Project DOI:doi: 10.21228/M8ND7K
Project Title:Metabolite and lipid profiling after early-life exposure to an endocrine disrupting chemical.
Project Type:Targeted and Untargeted MS analysis
Project Summary:Metabolic profiling in serum and liver tissue after early-life exposure to an endocrine disrupting chemical.
Institute:Baylor College of Medicine
Last Name:Walker
First Name:Cheryl
Address:1 Baylor Plaza, Houston, TX, 77030, USA
Email:Cheryl.walker@bcm.edu
Phone:713-798-8219

Subject:

Subject ID:SU001386
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Genotype Strain:Sprague Dawley
Age Or Age Range:70 days old
Gender:Male
Animal Animal Supplier:Harlan
Animal Housing:polycarbonate-free caging
Animal Light Cycle:14-hr light and 10-hr dark

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA094669ncB1BPA
SA094670ncB5BPA
SA094671ncB4BPA
SA094672ncB2BPA
SA094673ncB3BPA
SA094674ncV5vehicle
SA094675ncV4vehicle
SA094676ncV1vehicle
SA094677ncV2vehicle
SA094678ncV3vehicle
Showing results 1 to 10 of 10

Collection:

Collection ID:CO001381
Collection Summary:Blood was collected via cardiac puncture at the time of tissue harvest. For separating serum from the blood cells, the samples were allowed to clot at room temperature for 20-30 minutes, followed by centrifugation for 10 min at 1000 x g, and storage of the separated serum at -80°C.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR001401
Treatment Summary:Neonatal rats were treated with vehicle (sesame oil) or bisphenol A (BPA; 50 µg/kg dissolved in sesame oil) orally via pipette tip on post-natal days 1, 3, and 5. Littermates were randomly assigned to the treatment groups. BPA was obtained from the National Institute of Environmental Health Sciences (NIEHS). The dose and route of administration recapitulates human exposure to BPA. Tissue was harvested on postnatal day 70.

Sample Preparation:

Sampleprep ID:SP001394
Sampleprep Summary:Lipids were extracted using a modified Bligh-Dyer method. Fifty µL of serum and 25 mg of crushed liver was used for the extraction. The extraction was carried out using 2:2:2 volume ratio of water/methanol/dichloromethane at room temperature after spiking internal standards 17:0 LPC, 17:0 PC, 17:0 PE, 17:0 PG, 17:0 ceramide, 17:0 SM, 17:0PS, 17:0PA, 17:0 TAG, 17:0 MAG, 16:0/18:1 DAG, 17:0 CE. The organic layer was collected and completely dried under nitrogen. Before MS analysis, the dried extract was resuspended in 100 μL of Buffer B (10:5:85 Acetonitrile/water/Isopropyl alcohol) containing 10 mM NH4OAc and subjected to LC/MS. The lipidome was separated using reverse-phase chromatography.
Sampleprep Protocol Filename:unbiased.serum.MS.method.pdf

Combined analysis:

Analysis ID AN002184 AN002185
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Shimadzu Nexera-x2 Shimadzu Nexera-x2
Column Acquity HSS UPLC T3 column (1.8 μm particle 50 × 2.1 mm) 1.8 μm particle 50 × 2.1 mm
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name ABI Sciex 5600 TripleTOF ABI Sciex 5600 TripleTOF
Ion Mode POSITIVE NEGATIVE
Units peak intensity peak intensity

Chromatography:

Chromatography ID:CH001599
Instrument Name:Shimadzu Nexera-x2
Column Name:Acquity HSS UPLC T3 column (1.8 μm particle 50 × 2.1 mm)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001600
Instrument Name:Shimadzu Nexera-x2
Column Name:1.8 μm particle 50 × 2.1 mm
Chromatography Type:Reversed phase

MS:

MS ID:MS002031
Analysis ID:AN002184
Instrument Name:ABI Sciex 5600 TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:For data acquisition through LC/MS analysis, we used a Shimadzu CTO-20A Nexera X2 UHPLC system equipped with a degasser, binary pump, thermostatted auto sampler, and a column oven for chromatographic separation. The column heater temperature was set at 55°C. For lipid separation, the 5 uL of the lipid extract was injected into a 1.8 μm particle 50 × 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA) which heats to 55°C. Acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate was solvent A and acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate was solvent B. For chromatographic elution we used a linear gradient over a 20 min total run time, with 60% solvent A and 40% solvent B gradient in the first 10 minutes, then the gradient was ramped in a linear fashion to 100% solvent B which was maintained for 7 minutes. After that the system was switched back to 60% solvent B and 40% solvent A for 3 minutes. The flow rate used for these experiments was 0.4 mL/min and the injection volume was 5μL. The column was equilibrated for 3 min before the next injection and run at a flow rate of 0.4 mL/min for a total run time of 20 min. The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada). The column effluent was directed to the electrospray ionization source. The voltage of source was set to 5500 V for positive ionization and 4500 V for negative ionization mode, the declustering potential was set to 60 V, and the source temperature to 450oC for both modes. The curtain gas flow, nebulizer, and heater gas were set to 30, 40, and 45 units, respectively. The instrument performed one TOF MS survey scan (150 ms) and 15 MS/MS scans with a total duty cycle time of 2.4 s. The mass range in both modes was 50-1200 m/z. We controlled the acquisition of MS/MS spectra by data-dependent acquisition (DDA) function of the Analyst TF software (AB Sciex, Concord, Canada) with the following parameters: dynamic background subtraction, charge monitoring to exclude multiply charged ions and isotopes, and dynamic exclusion of former target ions for 9 s. Rolling collision energy spread was set whereby the software calculated the collision energy value to be applied as a function of m/z. Mass accuracy was maintained by the use of an automated calibrant delivery system interfaced to the second inlet of the DuoSpray source.
Ion Mode:POSITIVE
  
MS ID:MS002032
Analysis ID:AN002185
Instrument Name:ABI Sciex 5600 TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:For data acquisition through LC/MS analysis, we used a Shimadzu CTO-20A Nexera X2 UHPLC system equipped with a degasser, binary pump, thermostatted auto sampler, and a column oven for chromatographic separation. The column heater temperature was set at 55°C. For lipid separation, the 5 uL of the lipid extract was injected into a 1.8 μm particle 50 × 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA) which heats to 55°C. Acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate was solvent A and acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate was solvent B. For chromatographic elution we used a linear gradient over a 20 min total run time, with 60% solvent A and 40% solvent B gradient in the first 10 minutes, then the gradient was ramped in a linear fashion to 100% solvent B which was maintained for 7 minutes. After that the system was switched back to 60% solvent B and 40% solvent A for 3 minutes. The flow rate used for these experiments was 0.4 mL/min and the injection volume was 5μL. The column was equilibrated for 3 min before the next injection and run at a flow rate of 0.4 mL/min for a total run time of 20 min. The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada). The column effluent was directed to the electrospray ionization source. The voltage of source was set to 5500 V for positive ionization and 4500 V for negative ionization mode, the declustering potential was set to 60 V, and the source temperature to 450oC for both modes. The curtain gas flow, nebulizer, and heater gas were set to 30, 40, and 45 units, respectively. The instrument performed one TOF MS survey scan (150 ms) and 15 MS/MS scans with a total duty cycle time of 2.4 s. The mass range in both modes was 50-1200 m/z. We controlled the acquisition of MS/MS spectra by data-dependent acquisition (DDA) function of the Analyst TF software (AB Sciex, Concord, Canada) with the following parameters: dynamic background subtraction, charge monitoring to exclude multiply charged ions and isotopes, and dynamic exclusion of former target ions for 9 s. Rolling collision energy spread was set whereby the software calculated the collision energy value to be applied as a function of m/z. Mass accuracy was maintained by the use of an automated calibrant delivery system interfaced to the second inlet of the DuoSpray source.
Ion Mode:NEGATIVE
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