Summary of Study ST004256

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 PR002684. The data can be accessed directly via it's Project DOI: 10.21228/M8QG20 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST004256
Study TitleCentral carbon metabolites in Wild Type (WT) and dioxin response element (DRE) mice treated with TCDD
Study Summary2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) reprograms central carbon metabolism by switching pyruvate kinase expression from isoform M1 (Pkm1) to M2 (Pkm2) mediated by aryl hydrocarbon receptor (AhR) binding to a dioxin response element (DRE) located between exon 3 and 4 within the Pkm locus. To further investigate the consequences of Pkm isoform switching in TCDD elicited hepatotoxicity, we examined gene expression in primary hepatocytes isolated from mice with the Pkm locus DRE excised (PkmΔDRE) as well as metabolic changes in WT and PkmΔDRE mice treated with 30 µg/kg TCDD every 4 day for 28 days. While AHR target genes were comparably induced, some genes exhibited divergent expression patterns in PkmΔDREmice compared to wild-types following treatment with TCDD. Notably, antioxidant gene expression was delayed in PkmΔDRE hepatocytes. Metabolomic analysis also revealed differences in glycolytic, TCA cycle and pentose phosphate pathway metabolite levels in TCDD treated WT and PkmΔDRE liver extracts. In addition, amino acid metabolism and serine/glycine synthesis were also elevated, especially in PkmΔDRE. These findings indicate PKM2 induction affects the transcriptional and metabolic coordination of hepatic responses to TCDD.
Institute
Michigan State University
Last NameOrlowska
First NameKarina
Address1129 Farm Lane, Room 248, East Lansing, Michigan, 48824, USA
Emailorlowska@msu.edu
Phone5178842054
Submit Date2025-09-08
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-10-10
Release Version1
Karina Orlowska Karina Orlowska
https://dx.doi.org/10.21228/M8QG20
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002684
Project DOI:doi: 10.21228/M8QG20
Project Title:Central carbon metabolites in Wild Type (WT) and dioxin response element (DRE) mice
Project Type:Targeted MS
Project Summary:Central carbon metabolite changes were assessed in WT and PkmΔDRE mice treated with 30 µg/kg TCDD every 4 day for 28 days. Metabolomic analysis also revealed differences in glycolytic, TCA cycle and pentose phosphate pathway metabolite levels in TCDD treated WT and PkmΔDRE liver extracts. In addition, amino acid metabolism and serine/glycine synthesis were also elevated, especially in PkmΔDRE. These findings indicate PKM2 induction affects the transcriptional and metabolic coordination of hepatic responses to TCDD.
Institute:Michigan State University
Last Name:Orlowska
First Name:Karina
Address:1129 Farm Lane, Room 248, East Lansing, Michigan, 48824, USA
Email:orlowska@msu.edu
Phone:5178842054

Subject:

Subject ID:SU004408
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Gender:Male
Animal Animal Supplier:Charles Rivers Laboratories
Animal Housing:Innovive Innocage
Animal Light Cycle:12:12
Animal Feed:Harlan Teklad 8940, ad libitum
Animal Water:Innovive, ad libitum

Factors:

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

mb_sample_id local_sample_id Sample source Genotype Treatment
SA496767DRE_30_5Liver mutant TCDD
SA496768DRE_30_4Liver mutant TCDD
SA496769DRE_30_3Liver mutant TCDD
SA496770DRE_30_2Liver mutant TCDD
SA496771DRE_30_1Liver mutant TCDD
SA496772DRE_0_2Liver mutant Vehicle
SA496773DRE_0_5Liver mutant Vehicle
SA496774DRE_0_4Liver mutant Vehicle
SA496775DRE_0_3Liver mutant Vehicle
SA496776DRE_0_1Liver mutant Vehicle
SA496757WT_30_5Liver WT TCDD
SA496758WT_30_4Liver WT TCDD
SA496759WT_30_3Liver WT TCDD
SA496760WT_30_2Liver WT TCDD
SA496761WT_30_1Liver WT TCDD
SA496762WT_0_2Liver WT Vehicle
SA496763WT_0_5Liver WT Vehicle
SA496764WT_0_4Liver WT Vehicle
SA496765WT_0_3Liver WT Vehicle
SA496766WT_0_1Liver WT Vehicle
Showing results 1 to 20 of 20

Collection:

Collection ID:CO004401
Collection Summary:Liver Tissue was carefully excised and immediately frozen in liquid nitrogen.
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004417
Treatment Summary:Mice were orally gavaged with 0.1 mL of the test article (30 µg/kg TCDD) in vehicle (sesame oil) every 4 days for 28 days for a total of 7 administrations. First dose was administrated on PND 28.
Treatment Compound:2,3,7,8-Tetrachlorodibenzo-p-dioxin
Treatment Route:oral gavage
Treatment Dose:30 microgram per kilogram
Treatment Dosevolume:0.1 ml
Treatment Doseduration:every 4 days for 28 days
Treatment Vehicle:sesame oil
Animal Fasting:No
Animal Endp Euthanasia:Carbon dioxide asphyxiation

Sample Preparation:

Sampleprep ID:SP004414
Sampleprep Summary:Frozen liver samples were homogenized (Polytron PT2100, Kinematica) in methanol 500 μL of HPLC grade methanol, 200 μL of HPLC-grade water and 500 μL of HPLC-grade chloroform. Samples are vortexed for 10 minutes, then centrifuged at 4 °C 16,000xg for 15 minutes. The polar layer was then removed and dried under nitrogen gas. Extracted metabolites were then resuspended in 3% methanol containing 10 mM tributylamine (TBA).

Combined analysis:

Analysis ID AN007082
Chromatography ID CH005379
MS ID MS006779
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Xevo G2-XS UPLC/MS/MS
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Xevo-G2-XS
Ion Mode NEGATIVE
Units peak area/mg of tissues

Chromatography:

Chromatography ID:CH005379
Chromatography Summary:Chromatographic separation utilized an Acquity HSS T3 column (1.8 μm particle size, 2.1 mm × 150 mm). A binary solvent system was applied for gradient elution. The mobile phase A consisted of LC/MS-grade water containing 3% LC/MS-grade methanol, 10 mM tributylamine (TBA), and 15 mM acetic acid (pH 5.0 ± 0.05). Mobile phase B was composed of LC/MS-grade methanol (100%). A constant flow rate of 300 μl/min was maintained and the linear gradient employed was as follows: 0–1.5 min 100% A, 1.5–4 min increase from 0 to 20% B, 4–6. min maintain 80% A and 20% B, 6–10.5 min increase from 20 to 55% B, 10–13 min increase from 55 to 95% B, 13–15 min maintain 5% A and 95% B, 15–15.1 min decrease from 95 – 0% B, 15.1-18 min equilibration at 100% A. The column temperature was maintained at 40°C and sample volumes of 10 μL were injected.
Instrument Name:Waters Xevo G2-XS UPLC/MS/MS
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:40°C
Flow Gradient:0–1.5 min 0% B, 1.5–4 min increase from 0 to 20% B, 4–6 min maintain at 20% B, 6–10.5 min increase from 20 to 55% B, 10–13 min increase from 55 to 95% B, 13–15 min maintain at 95% B, 15–15.1 min decrease from 95 – 0% B, 15.1-18 min equilibration at 0% B
Flow Rate:300 μl/min
Solvent A:97% water/3% methanol; 10 mM tributylamine; 15 mM acetic acid (pH 5.0 ± 0.05)
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS006779
Analysis ID:AN007082
Instrument Name:Waters Xevo-G2-XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:Metabolite profiling was conducted by measuring relative abundance and high-resolution accurate mass spectrometry on a Xevo G2-XS QTof mass spectrometer (Waters, Eschborn, Germany). An 18-minute full-scan method was used to acquire data with m/z scan range from 50 to 1000. Signals were identified by retention time and accurate using MassLynx Version 4.2 (Waters).
Ion Mode:NEGATIVE
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