Summary of Study ST001309
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 | ST001309 |
| Study Title | Metabolite expression in liver after early life exposure to an endocrine disruptor at 240 days postnatal (part-I) |
| Study Type | Metabolite 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 |
| Department | Molecular and Cellular Biology |
| Laboratory | Center for Precision Environmental Health |
| Last Name | Walker |
| First Name | Cheryl |
| Address | 1 Baylor Plaza, Houston, TX, 77030, USA |
| Cheryl.walker@bcm.edu | |
| Phone | 713-798-8219 |
| Submit Date | 2020-01-27 |
| 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: | SU001383 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Genotype Strain: | Sprague Dawley |
| Age Or Age Range: | 240 days |
| Gender: | Male |
| Animal Animal Supplier: | Harlan |
| Animal Housing: | polycarbonate-free caging |
| Animal Light Cycle: | 14-hr light and 10-hr dark |
| Animal Feed: | Phytoestrogen Reduced II 18-5 (Ziegler Bros, Inc) or D09100301 (Research Diets, Inc) |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA094609 | HFD-BPA14 | BPA |
| SA094610 | HFD-BPA16 | BPA |
| SA094611 | HFD-BPA18 | BPA |
| SA094612 | HFD-BPA13 | BPA |
| SA094613 | HFD-BPA12 | BPA |
| SA094614 | HFD-VEH15 | vehicle |
| SA094615 | HFD-VEH18 | vehicle |
| SA094616 | HFD-VEH12 | vehicle |
| SA094617 | HFD-VEH14 | vehicle |
| SA094618 | HFD-VEH13 | vehicle |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO001378 |
| Collection Summary: | Liver tissue was harvested on post-natal day 240 after challenge with Western-style diet.Tissue was snap-frozen in liquid nitrogen. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR001398 |
| 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. At day 180, adult rats in both treatment groups were fed a diet high in fat (40% kcal), fructose (20% kcal) and cholesterol (2%) (Western-style diet) for 60 days (D09100301, Research Diets, Inc). Rats were fasted overnight prior to tissue collection. |
Sample Preparation:
| Sampleprep ID: | SP001391 |
| Sampleprep Summary: | Metabolites were extracted from crushed liver samples and a mouse liver pool was used for quality control. Twenty-five mg of crushed liver was used for the metabolic extraction. The extraction step started with the addition of 750 µL ice-cold methanol:water (4:1) containing 20 µL spiked internal standards to each tissue sample. Ice-cold chloroform and water were added in a 3:1 ratio for a final proportion of 1:4:3:1 water:methanol:chloroform:water. The organic (methanol and chloroform) and aqueous layers were mixed, dried and resuspended with 50:50 methanol: water. The extract was deproteinized using a 3kDa molecular filter (Amicon ultracel-3K Membrane; Millipore Corporation, Billerica, MA) and the filtrate was dried under vacuum (Genevac EZ-2plus; Gardiner, Stone Ridge, NY). Prior to mass spectrometry, the dried extracts were re-suspended in identical volumes of injection solvent composed of 1:1 water: methanol and were subjected to liquid chromatography-mass spectrometry. Fifty µl of sample was used for preparation. Internal standards were spiked into the samples. Then it was processed through a 3 kDa filter. After that, 50 µl of sample was diluted with 450 µl solvent (methanol: water = 50:50 v/v) and subjected to LC/MS analysis. The injection volume was 10 µl. For internal standards, high-performance liquid chromatography (HPLC)-grade acetonitrile, methanol, and water were procured from Burdick & Jackson (Morristown, NJ). Mass spectrometry-grade formic acid was purchased from Sigma-Aldrich (St Louis, MO). Calibration solution containing multiple calibrants in a solution of acetonitrile, trifluroacetic acid, and water was purchased from Agilent Technologies (Santa Clara, CA). Metabolites and internal standards, including N-acetyl Aspartic acid-d3, Tryptophan-15N2, Sarcosine-d3, Glutamic acid-d5, Thymine-d4, Gibberellic acid, Trans-Zeatine, Jasmonic acid, 15N Anthranilic acid, and Testosterone-d3, were purchased from Sigma-Aldrich (St. Louis, MO). Three LC- MS methods were used to separate metabolites. Method A: In ESI positive mode the HPLC column was waters X-bridge amide 3.5 µm, 4.6 x 100 mm (Waters, Milford, MA). Mobile phase A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient flow: 0-3 min 85% B; 3-12 min 30% B, 12-15 min 2% B, 16 min 95%B, followed by re-equilibration till the end of the gradient 23 min to the initial starting condition of 85% B. Flow rate of the solvents used for the analysis is 0.3 ml/min. Injection volume was 10 µL. Method B: In ESI negative mode the HPLC column was waters X-bridge amide 3.5 µm, 4.6 x 100 mm (Waters, Milford, MA). Mobile phase A and B were 20 mM ammonium acetate in water with pH 9.0 and 100% acetonitrile, respectively. Gradient flow: 0-3 min 85% B, 3-12 min 30% B, 12-15 min 2% B, 15-16 min 85% B followed by re-equilibration till the end of the gradient 23 min to the initial starting condition of 85% B. Flow rate of the solvents used for analysis is 0.3 ml/min. Injection volume was 10 µL. Method C: In ESI positive mode the HPLC column was Luna 3 µM NH2 100 A0 Chromatography column (Phenomenex, Torrance, CA). Mobile phase A and B were 20 mM ammonium acetate in water with pH 9.0 and 100% acetonitrile, respectively. Gradient flow: 0-3 min 85% B, 3-12 min 30% B, 12-15 min 2% B, 15-16 min 85% B followed by re-equilibration till the end of the gradient 23 min to the initial starting condition of 85% B. Flow rate of the solvents used for analysis is 0.3 ml/min. Injection volume was 10 µL. For data acquisition through LC/MS analysis, 10 µL of suspended samples were injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM). Source parameters were as follows: Gas temperature- 250°C; Gas flow- 14 l/min; Nebulizer - 20psi; Sheath gas temperature - 350°C; Sheath gas flow- 12 l/min; Capillary - 3000 V positive and 3000 V negative; Nozzle voltage- 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. The data acquired using Agilent mass hunter software and data was analyzed using mass hunter quantitative analysis software. |
| Sampleprep Protocol Filename: | Targeted.MS.method.pdf unbiased.liver.MS.method.pdf |
Combined analysis:
| Analysis ID | AN002178 | AN002179 | AN002180 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC |
| Chromatography system | Agilent 6495 QQQ | Agilent 6495 QQQ | Agilent 6495 QQQ |
| Column | Waters XBridge Amide (100 x 4.6mm,3.5um) | Waters XBridge Amide (100 x 4.6mm,3.5um) | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6495 QQQ | Agilent 6495 QQQ | Agilent 6495 QQQ |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | peak intensity | peak intensity | peak intensity |
Chromatography:
| Chromatography ID: | CH001593 |
| Instrument Name: | Agilent 6495 QQQ |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001594 |
| Instrument Name: | Agilent 6495 QQQ |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001595 |
| Instrument Name: | Agilent 6495 QQQ |
| Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002025 |
| Analysis ID: | AN002178 |
| Instrument Name: | Agilent 6495 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | For data acquisition through LC/MS analysis, 10 µL of suspended samples were injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM). Source parameters were as follows: Gas temperature- 250°C; Gas flow- 14 l/min; Nebulizer - 20psi; Sheath gas temperature - 350°C; Sheath gas flow- 12 l/min; Capillary - 3000 V positive and 3000 V negative; Nozzle voltage- 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. The data acquired using Agilent mass hunter software and data was analyzed using mass hunter quantitative analysis software. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002026 |
| Analysis ID: | AN002179 |
| Instrument Name: | Agilent 6495 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | For data acquisition through LC/MS analysis, 10 µL of suspended samples were injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM). Source parameters were as follows: Gas temperature- 250°C; Gas flow- 14 l/min; Nebulizer - 20psi; Sheath gas temperature - 350°C; Sheath gas flow- 12 l/min; Capillary - 3000 V positive and 3000 V negative; Nozzle voltage- 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. The data acquired using Agilent mass hunter software and data was analyzed using mass hunter quantitative analysis software. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002027 |
| Analysis ID: | AN002180 |
| Instrument Name: | Agilent 6495 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | For data acquisition through LC/MS analysis, 10 µL of suspended samples were injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM). Source parameters were as follows: Gas temperature- 250°C; Gas flow- 14 l/min; Nebulizer - 20psi; Sheath gas temperature - 350°C; Sheath gas flow- 12 l/min; Capillary - 3000 V positive and 3000 V negative; Nozzle voltage- 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. The data acquired using Agilent mass hunter software and data was analyzed using mass hunter quantitative analysis software. |
| Ion Mode: | POSITIVE |
