Summary of Study ST004035

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 PR002527. The data can be accessed directly via it's Project DOI: 10.21228/M80R9W This work is supported by NIH grant, U2C- DK119886.

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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 IDST004035
Study TitleSerum Metabolites at Defined Stages of Liver Disease
Study SummaryThe goal of this study was to reveal serum metabolome differences at defined stages of liver disease from fatty liver to hepatocellular carcinoma. This study investigates serum metabolomic alterations in a mouse model of non-alcoholic steatohepatitis (NASH) and HCC) using the STAM (Streptozotocin and High-Fat Diet) model. Male mice were administered streptozotocin (STZ) shortly after birth and subsequently fed a high-fat diet to induce liver disease progression resembling human NASH and HCC. Blood samples were collected at a defined disease stage , and serum was isolated for untargeted metabolomic profiling. Using LC-MS, we profiled the serum metabolites to identify disease-associated metabolic signatures. The study parameters include treatment condition (control vs. STAM), sample collection time (e.g., ZT8), and serum metabolite intensity values. Analysis revealed significant changes in pathways related to lipid metabolism, bile acid biosynthesis, amino acid metabolism, and energy homeostasis in the STAM group compared to controls. These metabolic alterations may reflect the systemic metabolic disturbances associated with NASH progression and HCC risk, providing potential biomarkers and therapeutic targets.
Institute
University of Texas Health Science Center at Houston
DepartmentIMM
LaboratoryMahan Lab
Last NameFekry
First NameBaharan
AddressThe Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), 1825 Pressler St, Houston TX 77030, USA.
EmailBaharan.Fekry@uth.tmc.edu
Phone18434693199
Submit Date2025-07-02
Analysis Type DetailLC-MS
Release Date2025-07-15
Release Version1
Baharan Fekry Baharan Fekry
https://dx.doi.org/10.21228/M80R9W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002527
Project DOI:doi: 10.21228/M80R9W
Project Title:Serum Metabolites at Defined Stages of Liver Disease
Project Summary:The present dataset comprises a total of 978 compounds of known identity (named biochemicals). Following log transformation and imputation of missing values, if any, with the minimum observed value for each compound, ANOVA contrasts were used to identify biochemicals that differed significantly between experimental groups. A summary of the numbers of biochemicals that achieved statistical significance (p≤0.05), as well as those approaching significance (0.05<p<0.10), is shown below. Analysis by two-way ANOVA identified biochemicals exhibiting significant interaction and main effects for experimental parameters of time and treatment. An estimate of the false discovery rate (q-value) is calculated to take into account the multiple comparisons that normally occur in metabolomic-based studies. For example, when analyzing 200 compounds, we would expect to see about 10 compounds meeting the p≤0.05 cut-off by random chance. The q-value describes the false discovery rate; a low q-value (q<0.10) is an indication of high confidence in a result. While a higher q-value indicates diminished confidence, it does not necessarily rule out the significance of a result. Other lines of evidence may be taken into consideration when determining whether a result merits further scrutiny. Such evidence may include a) significance in another dimension of the study, b) inclusion in a common pathway with a highly significant compound, or c) residing in a similar functional biochemical family with other significant compounds. Refer to the Appendix for general definitions and further descriptions of false discovery rate and other statistical tests used at Metabolon.
Institute:University of Texas Health Science Center at Houston
Department:IMM
Laboratory:Mahan Lab
Last Name:Fekry
First Name:Baharan
Address:The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), 1825 Pressler St, Houston TX 77030. USA.
Email:Baharan.Fekry@uth.tmc.edu
Phone:8434693199

Subject:

Subject ID:SU004181
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Sample source Group
SA466076Con_10wk_2liver Con_10wk
SA466077Con_10wk_5liver Con_10wk
SA466078Con_10wk_4liver Con_10wk
SA466079Con_10wk_3liver Con_10wk
SA466080Con_10wk_1liver Con_10wk
SA466081Con_16wk_5liver Con_16wk
SA466082Con_16wk_4liver Con_16wk
SA466083Con_16wk_3liver Con_16wk
SA466084Con_16wk_2liver Con_16wk
SA466085Con_16wk_1liver Con_16wk
SA466086Con_4wk_1liver Con_4wk
SA466087Con_4wk_2liver Con_4wk
SA466088Con_4wk_3liver Con_4wk
SA466089Con_4wk_5liver Con_4wk
SA466090Con_4wk_4liver Con_4wk
SA466091Con_7wk_5liver Con_7wk
SA466092Con_7wk_1liver Con_7wk
SA466093Con_7wk_4liver Con_7wk
SA466094Con_7wk_3liver Con_7wk
SA466095Con_7wk_2liver Con_7wk
SA466096STZ_10wk_4liver STZ_10wk
SA466097STZ_10wk_1liver STZ_10wk
SA466098STZ_10wk_2liver STZ_10wk
SA466099STZ_10wk_3liver STZ_10wk
SA466100STZ_10wk_5liver STZ_10wk
SA466101STZ_16wk_5liver STZ_16wk
SA466102STZ_16wk_4liver STZ_16wk
SA466103STZ_16wk_3liver STZ_16wk
SA466104STZ_16wk_2liver STZ_16wk
SA466105STZ_16wk_1liver STZ_16wk
SA466106STZ_4wk_4liver STZ_4wk
SA466107STZ_4wk_2liver STZ_4wk
SA466108STZ_4wk_5liver STZ_4wk
SA466109STZ_4wk_3liver STZ_4wk
SA466110STZ_4wk_1liver STZ_4wk
SA466111STZ_7wk_3liver STZ_7wk
SA466112STZ_7wk_1liver STZ_7wk
SA466113STZ_7wk_5liver STZ_7wk
SA466114STZ_7wk_4liver STZ_7wk
SA466115STZ_7wk_2liver STZ_7wk
Showing results 1 to 40 of 40

Collection:

Collection ID:CO004174
Collection Summary:A total of 40 serum samples were collected at the time of dissection, corresponding to ZT8 (Zeitgeber Time 8), from mice enrolled in an 8-group study modeling the progression from control to NASH, fibrosis, and HCC. Each group included 5 mice. Blood was collected via terminal cardiac puncture, and serum was isolated and snap-frozen, then stored at –80°C until analysis.
Sample Type:hepatocyte

Treatment:

Treatment ID:TR004190
Treatment Summary:Control mice received a vehicle (placebo) treatment, while STZ mice were administered streptozotocin (STZ) at 15 days of age to induce β-cell dysfunction. All mice were switched to a high-fat diet (HFD) at 4 weeks of age to promote progression to NASH, fibrosis, and HCC across timepoints.

Sample Preparation:

Sampleprep ID:SP004187
Sampleprep Summary:Serum samples were thawed on ice and prepared following Metabolon’s standard protocols. Protein precipitation was carried out using methanol under vigorous shaking, followed by centrifugation to extract metabolites. The resulting supernatants were split into multiple aliquots for analysis by LC/MS and GC/MS platforms. All samples were randomized prior to processing to reduce technical bias.

Chromatography:

Chromatography ID:CH005070
Chromatography Summary:Low pH polar (LC/MS Pos early)
Instrument Name:Thermo Dionex ICS-5000+
Column Name:Waters XBridge BEH C18 (100 x 2.1 mm, 3.5 μm)
Column Temperature:40°C-50°C
Flow Gradient:Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006673
Analysis Type:MS
Chromatography ID:CH005070
Num Factors:8
Num Metabolites:978
Units:LC/MS Peak intensity
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