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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001312 |
| Study Title | Lipid expression in serum after early lifer exposure to an endocrine disruptor at 70 days postnatal (part-III) |
| Study Type | Lipid expression after chemical exposure versus control. |
| Study Summary | Our 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 Name | Walker |
| First Name | Cheryl |
| Address | 1 Baylor Plaza |
| Cheryl.walker@bcm.edu | |
| Phone | 7137988219 |
| Submit Date | 2020-01-24 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Num Males | 10 |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-03-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA094669 | ncB1 | BPA |
| SA094670 | ncB5 | BPA |
| SA094671 | ncB4 | BPA |
| SA094672 | ncB2 | BPA |
| SA094673 | ncB3 | BPA |
| SA094674 | ncV5 | vehicle |
| SA094675 | ncV4 | vehicle |
| SA094676 | ncV1 | vehicle |
| SA094677 | ncV2 | vehicle |
| SA094678 | ncV3 | vehicle |
| 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 |
Chromatography:
| Chromatography ID: | CH001599 |
| Instrument Name: | Shimadzu Nexera-x2 |
| Column Name: | Acquity HSS UPLC T3 (50 x 2.1mm,1.8um) |
| Column Temperature: | 55 |
| Flow Gradient: | 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. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 40% acetonitrile/60% water; 10 mM ammonium acetate |
| Solvent B: | 10% acetonitrile/5% water/85% isopropanol; 10 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001600 |
| Instrument Name: | Shimadzu Nexera-x2 |
| Column Name: | 1.8 μm particle 50 × 2.1 mm |
| Column Temperature: | 55 |
| Flow Gradient: | 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. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 40% acetonitrile/60% water; 10 mM ammonium acetate |
| Solvent B: | 10% acetonitrile/5% water/85% isopropanol; 10 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN002184 |
| Analysis Type: | MS |
| Chromatography ID: | CH001599 |
| Num Factors: | 2 |
| Num Metabolites: | 249 |
| Units: | peak intensity |
| Analysis ID: | AN002185 |
| Analysis Type: | MS |
| Chromatography ID: | CH001600 |
| Num Factors: | 2 |
| Num Metabolites: | 233 |
| Units: | peak intensity |
