Summary of Study ST003738
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 PR002324. The data can be accessed directly via it's Project DOI: 10.21228/M87C17 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 | ST003738 |
| Study Title | Impact of Trans-Fatty acids on renal health in mice with partial Tgfβ3 deletion: a Metabolomic and Lipidomic analysis |
| Study Type | Multiplatform non-targeted metabolomics |
| Study Summary | Trans-fatty acids, prevalent in Western diets, contribute to the onset and progression of renal damage. This study investigates the effects of trans-fat consumption on kidney health using a comprehensive approach encompassing metabolomics, lipidomics, molecular, and cellular analyses. We analyzed both wild-type mice and mice with partial Tgfβ3 deletion, a model for pre-existing renal damage. In control animals, the trans-fat diet induced significant dysregulation in renal lipid metabolism. Omic analyses revealed a reduction in triglycerides and an increase in plasmalogens, which are associated with cellular protection and signaling. Furthermore, upregulation of TCA cycle metabolites, malic and fumaric acids, indicated mitochondrial dysfunction. In mice with partial Tgfβ3 deletion, trans-fat consumption exacerbated renal fibrosis, and further depleted triglycerides and plasmalogens. Despite similar lipid profiles in both groups, Tgfβ3-deleted mice exhibited larger lipid droplets and worsened renal damage, including a notable reduction in taurine levels. This study underscores the value of detailed metabolic profiling to uncover mechanisms driving renal dysfunction linked to harmful dietary habits and genetic mutations. |
| Institute | Universidad Rey Juan Carlos |
| Department | Basic Sciences of Health |
| Laboratory | Lipobeta |
| Last Name | Lanzon |
| First Name | Borja |
| Address | Avenida de Atenas S/N |
| borja.lanzon@urjc.es | |
| Phone | 663692554 |
| Submit Date | 2024-12-16 |
| Num Groups | 4 |
| Total Subjects | 28 |
| Num Males | 28 |
| Study Comments | Study is composed of 4 groups of mice: wild-type on control diet (WT-CD), wild-type on trans diet (WT-HFD), heterozygous TGFBeta 3 on control diet (HZ-CD) and heterozygous TGFBeta 3 on trans diet (HZ-HFD) |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, d |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2025-03-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002324 |
| Project DOI: | doi: 10.21228/M87C17 |
| Project Title: | Impact of Trans-Fatty acids on renal health in mice with partial Tgfβ3 deletion: a Metabolomic and Lipidomic analysis |
| Project Type: | Multiplatform non-targeted metabolomics |
| Project Summary: | Trans-fatty acids, prevalent in Western diets, contribute to the onset and progression of renal damage. This study investigates the effects of trans-fat consumption on kidney health using a comprehensive approach encompassing metabolomics, lipidomics, molecular, and cellular analyses. We analyzed both wild-type mice and mice with partial transforming growth factor beta 3 (Tgfβ3) deletion, a model for pre-existing renal damage. In control animals, the trans-fat diet induced significant dysregulation in renal lipid metabolism. Omic analyses revealed a reduction in triglycerides and an increase in plasmalogens, which are associated with cellular protection and signaling. Furthermore, upregulation of Tricarboxylic acid cycle (TCA) metabolites, malic and fumaric acids, indicated mitochondrial dysfunction. In mice with partial Tgfβ3 deletion, trans-fat consumption exacerbated renal fibrosis, and further depleted triglycerides and plasmalogens. Despite similar lipid profiles in both groups, Tgfβ3-deleted mice exhibited larger lipid droplets and worsened renal damage, including a notable reduction in taurine levels. This study underscores the value of detailed metabolic profiling to uncover mechanisms driving renal dysfunction linked to harmful dietary habits and genetic mutations. |
| Institute: | Universidad Rey Juan Carlos |
| Department: | Basic Sciences of Health |
| Laboratory: | Lipobeta |
| Last Name: | Lanzon |
| First Name: | Borja |
| Address: | Avenida de Atenas S/N |
| Email: | borja.lanzon@urjc.es |
| Phone: | 663692554 |
Subject:
| Subject ID: | SU003870 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 16 weeks |
| Weight Or Weight Range: | 26 to 32 g |
| Gender: | Male |
| Animal Feed: | Control diet: D12450B, Research Diets. Trans diet: TD.07011, ENVIGO |
| Species Group: | 4 groups: wild-type animals on control diet (WT-CD), wild-type on trans diet (WT-HFD), Heterozygous TGFBeta 3 on control diet (HZ-CD) and Heterozygous TGFBeta 3 on trans diet (HZ-HFD) |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Diet |
|---|---|---|---|
| SA407820 | 98 HZCD | Heterozygous | Control |
| SA407821 | 119 HZCD | Heterozygous | Control |
| SA407822 | 25 HZCD | Heterozygous | Control |
| SA407823 | 269 HZCD | Heterozygous | Control |
| SA407824 | 127 HZCD | Heterozygous | Control |
| SA407825 | 130 HZCD | Heterozygous | Control |
| SA407826 | 267 HZCD | Heterozygous | Control |
| SA407827 | 81 HZHFD | Heterozygous | Transfat |
| SA407828 | 139 HZHFD | Heterozygous | Transfat |
| SA407829 | 131 HZHFD | Heterozygous | Transfat |
| SA407830 | 96 HZHFD | Heterozygous | Transfat |
| SA407831 | 95 HZHFD | Heterozygous | Transfat |
| SA407832 | 136 HZHFD | Heterozygous | Transfat |
| SA407833 | 123 HZHFD | Heterozygous | Transfat |
| SA407834 | QC5 | QC | QC |
| SA407835 | QC4 | QC | QC |
| SA407836 | QC3 | QC | QC |
| SA407837 | QC2 | QC | QC |
| SA407838 | QC1 | QC | QC |
| SA407839 | 128 WTCD | Wild-Type | Control |
| SA407840 | 92 WTCD | Wild-Type | Control |
| SA407841 | 132 WTCD | Wild-Type | Control |
| SA407842 | 251 WTCD | Wild-Type | Control |
| SA407843 | 120 WTCD | Wild-Type | Control |
| SA407844 | 79 WTCD | Wild-Type | Control |
| SA407845 | 129 WTCD | Wild-Type | Control |
| SA407846 | 83 WTHFD | Wild-Type | Transfat |
| SA407847 | 91 WTHFD | Wild-Type | Transfat |
| SA407848 | 29 WTHFD | Wild-Type | Transfat |
| SA407849 | 133 WTHFD | Wild-Type | Transfat |
| SA407850 | 134 WTHFD | Wild-Type | Transfat |
| SA407851 | 138 WTHFD | Wild-Type | Transfat |
| SA407852 | 124 WTHFD | Wild-Type | Transfat |
| Showing results 1 to 33 of 33 |
Collection:
| Collection ID: | CO003863 |
| Collection Summary: | Kidney samples were powdered with mortar and pestle. Initially, approximately 60 mg of each pulverized kidney sample was collected, then 50% Methanol: H2O (1 mg tissue: 10 μL solvent) was added to each sample. After that, samples were homogenized using a Qiagen TissueLyser LT system (Hilden, Germany). Next, 100 μL of each kidney homogenate was vigorously mixed (vortex 2 min) with 320 μL of methanol. Subsequently, 80 μL of MTBE was added to each sample to extract the lipid fraction from the kidneys. The samples were vigorously mixed for one hour at room temperature, and then centrifuged (4000 g, 20 min, 20°C) to facilitate phase separation. |
| Sample Type: | Kidney |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003879 |
| Treatment Summary: | The study focused on metabolic, histological, and metabolomic alterations induced by a trans-fat-rich diet using wild-type C57Bl/6J mice, starting at 4 weeks old to 16 weeks. Mice were split into groups with a control diet, CD, (10% fat, D12450B, Research Diets, USA) or a high trans-fat diet, TFD, (29% fat, 54.4% total kcal, TD.07011, ENVIGO, USA), containing 24% saturated, 61% monounsaturated, and 15% polyunsaturated fats. To further evaluate the renal effects of the TFD, Tgfβ3 heterozygous mice (Tgfβ3+/-) were also studied alongside wild-type mice (Tgfβ3+/+), with both groups fed either a CD or TFD from 4 to 16 weeks of age. Complete deletion of both Tgfβ3 alleles is lethal. This animal model were grouped with the control or the trans-fat diets. After 16 weeks of age, Kidneys were collected and stored at -80°C. Kidney homogenate was prepared by adding cold (−20 °C) methanol/water (1:1, v/v), (1:10 tissue/solvent). Tissue disruption was achieved with Tissue- Lyser LT homogenizer (Qiagen, Germany) for metabolite extraction. |
Sample Preparation:
| Sampleprep ID: | SP003876 |
| Sampleprep Summary: | Depending on the specific metabolomic analysis, the samples were prepared as follows: LC-MS Analysis: 90 μL of the supernatant from each sample was transferred to chromatography vials. 45 μL was used for analysis in positive ionization mode (+), and another 45 μL was used for analysis in negative ionization mode. The supernatants were directly injected into the system for analysis. For GC−MS analysis, 300 μL of supernatant was evaporated to dryness (SpeedVac Concentrator System, Thermo Fisher Scientific, Waltham, MA). Methoxymation was then performed with 20 μL of O-methoxyamine hydrochloride (15 mg/mL in pyridine) and vigorously vortex-mixed for 5 min. Vials were then incubated in darkness at room temperature for 16 h. For silylation, 20 μL of BSTFA/TMCS (99:1) was added and vortex-mixed for 5 min, and capped vials were placed in the oven at 70 °C for 1 h. Finally, 100 μL of heptane containing tricosane (10 ppm) as internal standard (IS) was added to each vial prior to injection. For LC−MS analysis, 90 μL of supernatant was transferred to an ultra-high-performance liquid chromatography−mass spectrometry. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH004660 |
| Chromatography Summary: | LC-MS (+) A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Poroshell 120 Infinity Lab EC-C8 (2.1 x 150 mm, 2.7 µm) (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (10 mM ammonium formate in Milli-Q water) and mobile phase B (10 mM ammonium formate in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent InfinityLab Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) |
| Column Temperature: | 60 |
| Flow Gradient: | gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 10 mM ammonium formate |
| Solvent B: | 85% methanol/15% isopropanol; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004661 |
| Chromatography Summary: | LC-MS (-) A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Poroshell 120 Infinity Lab EC-C8 (2.1 x 150 mm, 2.7 µm) (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (10 mM ammonium formate in Milli-Q water) and mobile phase B (10 mM ammonium formate in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent InfinityLab Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) |
| Column Temperature: | 60 |
| Flow Gradient: | gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 85% methanol/15% isopropanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004662 |
| Chromatography Summary: | GC-MS An Agilent GC instrument (7890A) coupled to an inert mass spectrometer with triple-Axis detector (5975C, Agilent Technologies) was used for kidney tissue fingerprinting. Briefly, 1 μL of derivatized samples were injected by an Agilent autosampler (7693). Samples were automatically injected in split mode (split ratio 1:12), into an Agilent ultra-inert deactivated glass wool split liner. Compound separation was achieved using a pre-column (10 m J&W integrated with Agilent 122-5532G) combined with a GC column DB5-MS (length, 30m; inner diameter, 0.25 mm; and 0.25 μm film of 95% dimethyl/5% diphenylpolysiloxane). The flow rate of helium carrier gas was constant at 0.938 mL/min through the column. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 minutes was performed. The column oven temperature was initially set at 60°C (maintained for 1 minute), then raised by 10°C/min until it reached 325°C, and then was held at this temperature for 10 minutes before cooling down. The injector and the transfer line temperatures were established at 250°C and 280°C, respectively. The injector and the transfer line temperatures were established at 250°C and 280°C, respectively. |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | Programmed temperature gradient: The column oven temperature was initially set at 60°C (maintained for 1 minute), then raised by 10°C/min until it reached 325°C, and then was held at this temperature for 10 minutes before cooling down. |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN006136 |
| Analysis Type: | MS |
| Chromatography ID: | CH004660 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003738_AN006136_Results.txt |
| Units: | arbitrary units, a.u. |
| Analysis ID: | AN006137 |
| Analysis Type: | MS |
| Chromatography ID: | CH004661 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003738_AN006137_Results.txt |
| Units: | arbitrary units, a.u. |
| Analysis ID: | AN006138 |
| Analysis Type: | MS |
| Chromatography ID: | CH004662 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003738_AN006138_Results.txt |
| Units: | arbitrary units, a.u. |
