Summary of Study ST003038
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 PR001890. The data can be accessed directly via it's Project DOI: 10.21228/M8DQ64 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST003038 |
| Study Title | Untargeted lipidomics of WT and Cyp2c44(-/-) mice liver. |
| Study Type | Untargeted Lipidomics |
| Study Summary | Cytochrome P450 epoxygenase Cyp2c44 and their metabolite epoxyeicosatrienoic acids or EETs promotes insulin sensitivity. Mice lacking Cyp2c44 exhibits hepatic insulin resistance. Insulin resistance is also intricately related to increased hepatic lipid accumulation and hyperlipidemia. Interestingly, Cyp2c44(-/-) mice in standard chow diet had significantly increased hepatic and plasma lipid levels compared to wild-type mice. To identify the nature of these lipids, with a focus on fatty acids, we performed lipidomic analysis of liver homogenates from SD-fed WT and Cyp2c44(-/-) mice. We identified 2425 lipids (1152 in negative mode and 1273 in positive mode) that passed both quality control filters set as 25% for QC RSD and 10% for QC/blank ratio. Principal component analysis revealed two distinct lipid clusters in livers of WT and Cyp2c44(-/-) mice. Heatmap analysis revealed a hierarchical clustering of significant differences occurring in lipid species between WT and Cyp2c44(-/-) livers. Volcano plot analysis of the 1152 lipids identified in the negative mode (which contain fatty acids) revealed 160 lipid species upregulated, 61 downregulated, and 931 not significantly changed in Cyp2c44(-/-) livers compared to WT livers. Analysis of fatty acids classes in negative mode identified a total of 146 fatty acids, with 49 upregulated, 3 downregulated and 94 unchanged in Cyp2c44(-/-) compared to WT livers. Among the fatty acids that are significantly upregulated in the livers of Cyp2c44(-/-), we detected the saturated fatty acids palmitic acid; the monosaturated oleic acid; and the polyunsaturated arachidonic, linoleic, eicosapentaenoic and docosahexaenoic acids. Importantly, arachidonic acid is the major substrate of Cyp2c epoxygenases, although linoleic, eicosapentaenoic and docosahexaenoic acids are also efficient alternative substrates. We thus hypothesized that Cyp2c44 also governs hepatic lipid metabolism. |
| Institute | Vanderbilt University Medical Center |
| Last Name | Ghoshal |
| First Name | Kakali |
| Address | B-3106 Medical Center North, 1161 21st Ave South, Nashville, TN 37232 |
| kakali.ghoshal@vumc.org | |
| Phone | 615-3224635 |
| Submit Date | 2023-12-11 |
| Num Groups | 2 |
| Total Subjects | 9 |
| Num Males | 9 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-01-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001890 |
| Project DOI: | doi: 10.21228/M8DQ64 |
| Project Title: | Untargeted lipidomics of WT and Cyp2c44(-/-) mice liver. |
| Project Type: | Untargeted Lipidomics |
| Project Summary: | Cytochrome P450 epoxygenase Cyp2c44 and their metabolite epoxyeicosatrienoic acids or EETs promotes insulin sensitivity. Mice lacking Cyp2c44 exhibits hepatic insulin resistance. Insulin resistance is also intricately related to increased hepatic lipid accumulation and hyperlipidemia. Interestingly, Cyp2c44(-/-) mice in standard chow diet had significantly increased hepatic and plasma lipid levels compared to wild-type mice. To identify the nature of these lipids, with a focus on fatty acids, we performed lipidomic analysis of liver homogenates from SD-fed WT and Cyp2c44(-/-) mice. We identified 2425 lipids (1152 in negative mode and 1273 in positive mode) that passed both quality control filters set as 25% for QC RSD and 10% for QC/blank ratio. Principal component analysis revealed two distinct lipid clusters in livers of WT and Cyp2c44(-/-) mice. Heatmap analysis revealed a hierarchical clustering of significant differences occurring in lipid species between WT and Cyp2c44(-/-) livers. Volcano plot analysis of the 1152 lipids identified in the negative mode (which contain fatty acids) revealed 160 lipid species upregulated, 61 downregulated, and 931 not significantly changed in Cyp2c44(-/-) livers compared to WT livers. Analysis of fatty acids classes in negative mode identified a total of 146 fatty acids, with 49 upregulated, 3 downregulated and 94 unchanged in Cyp2c44(-/-) compared to WT livers. Among the fatty acids that are significantly upregulated in the livers of Cyp2c44(-/-), we detected the saturated fatty acids palmitic acid; the monosaturated oleic acid; and the polyunsaturated arachidonic, linoleic, eicosapentaenoic and docosahexaenoic acids. Importantly, arachidonic acid is the major substrate of Cyp2c epoxygenases, although linoleic, eicosapentaenoic and docosahexaenoic acids are also efficient alternative substrates. We thus hypothesized that Cyp2c44 also governs hepatic lipid metabolism. |
| Institute: | Vanderbilt University Medical Center |
| Department: | Nephrology |
| Last Name: | Ghoshal |
| First Name: | Kakali |
| Address: | B-3106 Medical Center North, 1161 21st Ave South, Nashville, TN 37232 |
| Email: | kakali.ghoshal@vumc.org |
| Phone: | 615-322-7729 |
Subject:
| Subject ID: | SU003152 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 12 weeks |
| Weight Or Weight Range: | 25 g |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA329857 | POS_09 | 2c44KO |
| SA329858 | POS_10 | 2c44KO |
| SA329859 | NEG_06 | 2c44KO |
| SA329860 | POS_08 | 2c44KO |
| SA329861 | NEG_07 | 2c44KO |
| SA329862 | POS_07 | 2c44KO |
| SA329863 | NEG_10 | 2c44KO |
| SA329864 | NEG_09 | 2c44KO |
| SA329865 | NEG_08 | 2c44KO |
| SA329866 | POS_06 | 2c44KO |
| SA329867 | NEG_05 | WT |
| SA329868 | NEG_04 | WT |
| SA329869 | NEG_01 | WT |
| SA329870 | POS_03 | WT |
| SA329871 | POS_02 | WT |
| SA329872 | POS_04 | WT |
| SA329873 | POS_05 | WT |
| SA329874 | NEG_02 | WT |
| SA329875 | POS_01 | WT |
| SA329876 | NEG_03 | WT |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO003145 |
| Collection Summary: | 100 mg of mouse livers were collected from standard chow diet fed WT and Cyp2c44(-/-) mice. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR003161 |
| Treatment Summary: | Experiments conducted in mice were approved by the Vanderbilt Institutional Animal Care and Use Committee. Male 129/SvJ wild-type (WT) and Cyp2c44(-/-) mice littermates were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–accredited facility. Mice were generated and maintained as described previously (Ghoshal K et al, Diabetes, 2021, doi: 10.2337/db21-0298). Mice were fed SD (~14% fat Purina Laboratory Rodent 5001) up to 12 weeks of age until euthanized to collect livers. |
Sample Preparation:
| Sampleprep ID: | SP003158 |
| Sampleprep Summary: | Mouse liver (100 mg) was homogenized in 500 µl PBS using FisherBrand BeadMill. Homogenates were spiked with 10 µl SPLASH-lipidomics internal standard mix (Avanti Polar Lipids/CRODA), transferred to glass tubes and extracted using the method of Bligh and Dyer. Lipid extracts were evaporated under a gentle stream of nitrogen gas and resuspended in 100 µl of HPLC-grade methanol and chloroform (9:1 ratio). Discovery lipidomics were performed using a Vanquish ultrahigh performance liquid chromatography (UHPLC) system interfaced to a Q Exactive HF quadrupole/orbitrap mass spectrometer (Thermo Fisher Scientific) operating in data-dependent mode. Lipid extracts (5 µl) were injected in both positive and negative ESI modes. Pooled QCs were injected to assess the performance of the LC and MS instruments at the beginning, middle and at the end of each sequence. |
Combined analysis:
| Analysis ID | AN004984 | AN004985 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peakarea | peakarea |
Chromatography:
| Chromatography ID: | CH003765 |
| Chromatography Summary: | MSRC Lipidomics LC method |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | Linear gradient from 20% B to 100% B over 7 minutes |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM Ammonium formate, pH ~3 |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM Ammonium formate, pH ~3 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004724 |
| Analysis ID: | AN004984 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS was operating in data-dependent mode (Top7); Raw data data were processed with MS-DIAL version 4.70 in POS-lipidomics mode. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004725 |
| Analysis ID: | AN004985 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS was operating in data-dependent mode (Top7); Raw data data were processed with MS-DIAL version 4.70 in NEG-lipidomics mode. |
| Ion Mode: | NEGATIVE |
