Summary of Study ST003311
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 PR002059. The data can be accessed directly via it's Project DOI: 10.21228/M8G533 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 | ST003311 |
Study Title | Complementary Omics Analyses of The Brain Of A Kainic Acid Epilepsy Model Reveal Alterations In Purine And Energy Metabolism With Metabolic Implications for miRNA Cargos Within Milk-Exosomes |
Study Summary | Augmentations in energy and glucose metabolism have been widely implicated in epilepsy, a neurological disorder that manifests as seizures. Evaluating the metabolic underpinnings of epilepsy using systems approaches to identify potential treatment targets will especially benefit ~30% of patients that struggle with drug-resistant epilepsy. Recently, bovine milk-derived exosomes and their associated miRNA cargos were demonstrated to be bioavailable in the brain, improve spatial learning, and decrease seizure severity. Here, we assessed the metabolic changes associated with epilepsy and this exosome diet on brain tissue isolated from a kainic acid mouse model of epilepsy via metabolomics and proteomics. Mice fed either an RNA-sufficient exosome diet (ERS) or an RNA-insufficient exosome diet (ERD). After dietary interventions, mice were injected with kainic acid (KA+) or vehicle solution (KA-) (n=24; n=6 in each category). We show that central carbon, purine, and redox metabolism pathways were primarily affected by seizures in addition to relatively understudied pathways such as hexosamine and nicotinamide salvage. We also show that the interaction effects of dietary exosomes and their associated miRNAs were most prominent in the presence of seizure. Proteomics data revealed a correlation of proteins and metabolites related to glycolytic and energy production pathways, implicating flux. |
Institute | University of Nebraska-Lincoln |
Last Name | Alicia |
First Name | Johnson |
Address | 433 Bolivar Street New Orleans, LA 70112 |
jadameclab@gmail.com | |
Phone | (504) 568-1610 |
Submit Date | 2024-06-19 |
Num Groups | 4 |
Total Subjects | 24 |
Study Comments | Raw metabolite values (with no processing) have been given. |
Raw Data Available | Yes |
Raw Data File Type(s) | d |
Analysis Type Detail | GC-MS |
Release Date | 2024-12-19 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR002059 |
Project DOI: | doi: 10.21228/M8G533 |
Project Title: | GCMS Metabolomics of the whole brain of a mouse model of epilepsy fed a diet of milk exosomes replete with miRNA |
Project Summary: | This project examines the metabolic changes associated with seizures in a kainic acid model of epilepsy in mice. Previously, mice fed a diet including milk exosomes replete with miRNA showed lower seizure severity than mice that were fed a diet that did not include the milk-exosome miRNAs. As a result we also examined metabolic changes associated with this diet and its impact on seizure occurrence and severity. |
Institute: | University of Nebraska-Lincoln |
Last Name: | Alicia |
First Name: | Johnson |
Address: | 433 Bolivar Street New Orleans, LA 70112 |
Email: | jadameclab@gmail.com |
Phone: | 5045681610 |
Subject:
Subject ID: | SU003432 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Gender: | Male and female |
Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Diet | Treatment |
---|---|---|---|---|
SA358875 | sampleblk3 | blank | NA | NA |
SA358876 | sampleblk2 | blank | NA | NA |
SA358877 | sampleblk1 | blank | NA | NA |
SA358878 | ctrl_F2 | brain tissue | ERD | No Seizure |
SA358879 | ctrl_F1 | brain tissue | ERD | No Seizure |
SA358880 | ctrl_M1 | brain tissue | ERD | No Seizure |
SA358881 | ctrl_F3 | brain tissue | ERD | No Seizure |
SA358882 | ctrl_M3 | brain tissue | ERD | No Seizure |
SA358883 | ctrl_M2 | brain tissue | ERD | No Seizure |
SA358884 | XO-_KA+_M3 | brain tissue | ERD | Seizure |
SA358885 | XO-_KA+_M2 | brain tissue | ERD | Seizure |
SA358886 | XO-_KA+_M1 | brain tissue | ERD | Seizure |
SA358887 | XO-_KA+_F3 | brain tissue | ERD | Seizure |
SA358888 | XO-_KA+_F2 | brain tissue | ERD | Seizure |
SA358889 | XO-_KA+_F1 | brain tissue | ERD | Seizure |
SA358890 | XO+_KA-_M3 | brain tissue | ERS | No Seizure |
SA358891 | XO+_KA-_M2 | brain tissue | ERS | No Seizure |
SA358892 | XO+_KA-_M1 | brain tissue | ERS | No Seizure |
SA358893 | XO+_KA-_F3 | brain tissue | ERS | No Seizure |
SA358894 | XO+_KA-_F2 | brain tissue | ERS | No Seizure |
SA358895 | XO+_KA-_F1 | brain tissue | ERS | No Seizure |
SA358896 | plus_F1 | brain tissue | ERS | Seizure |
SA358897 | plus_M3 | brain tissue | ERS | Seizure |
SA358898 | plus_F2 | brain tissue | ERS | Seizure |
SA358899 | plus_M2 | brain tissue | ERS | Seizure |
SA358900 | plus_M1 | brain tissue | ERS | Seizure |
SA358901 | plus_F3 | brain tissue | ERS | Seizure |
SA358902 | QC4 | pooled quality control | NA | NA |
SA358903 | QC2 | pooled quality control | NA | NA |
SA358904 | QC1 | pooled quality control | NA | NA |
SA358905 | PreQC2 | pooled quality control | NA | NA |
SA358906 | PreQC1 | pooled quality control | NA | NA |
SA358907 | PostQC1 | pooled quality control | NA | NA |
SA358908 | Post QC2 | pooled quality control | NA | NA |
SA358909 | QC3 | pooled quality control | NA | NA |
Showing results 1 to 35 of 35 |
Collection:
Collection ID: | CO003425 |
Collection Summary: | Whole brain was harvested, ground using a mortar and pestle constantly cooled with liquid nitrogen and stored at -80°C until later extraction. |
Sample Type: | Brain |
Treatment:
Treatment ID: | TR003441 |
Treatment Summary: | Studies were done in female (n=3 per condition) and male (n=3 per condition) C57BL/6J mice. Mice aged 3 weeks were fed an exosome miRNA sufficient (ERS) or an exosome miRNA depleted diet (ERD) for 18 weeks. ERS and ERD diets fed to mice were isolated and prepared as previously described. this protocol has been deposited in the EV-Track database (EV-TRACK ID:EV210338, https://evtrack.org). To study seizure activity, mice were treated with 25 mg/kg of kainic acid via subcutaneous injection. Mice were scored for seizure severity two hours before they were euthanized. Mice were euthanized via transcardial perfusion (1). 1. Zhou, F., Ebea, P., Mutai, E., Wang, H., Sukreet, S., Navazesh, S., Dogan, H., Li, W., Cui, J., Ji, P., Ramirez, D. M. O., & Zempleni, J. (2022). Small Extracellular Vesicles in Milk Cross the Blood-Brain Barrier in Murine Cerebral Cortex Endothelial Cells and Promote Dendritic Complexity in the Hippocampus and Brain Function in C57BL/6J Mice. Frontiers in nutrition, 9, 838543. https://doi.org/10.3389/fnut.2022.838543 |
Sample Preparation:
Sampleprep ID: | SP003439 |
Sampleprep Summary: | Briefly, 500 µL of methanol, 30 µL of ribitol (0.2 mg/mL in water), and ~100 µL of glass beads were added to 25 mg (±1 mg) of tissue. Tissues were homogenized for 8 minutes at high speed (power setting of 9) in a bullet blender (Next Advance, NY) at 4°C. After centrifugation at 14,000 xg for 10 minutes at 4°C, 400 µL of this homogenate was transferred to a clean Eppendorf tube to be heated at 70°C for 15 minutes. Following heating, samples were centrifuged for 10 minutes at 18,400 xg and 350 µL of sample transferred to a clean Eppendorf tube containing 350 µL of H2O and 175 µL of CHCl3. This was a final ratio of 9:11:5 (MeOH:H2O:CHCl3). Samples were vortexed and then centrifuged for 30 minutes at 1,500 xg to further separate phases. Six hundred microliters of the top, aqueous layer was dried in a speed vacuum at room temperature and stored at -80°C. For polar analysis via GC-MS, derivatization was done. Briefly, 40 µL of methoxyaminhydrochloride (20 mg/ml in pyridine) was added to the dried sample and incubated for 2 hours at 37ºC in a shaker. After, 70 µL of N-methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) mixture (1 mL MSTFA and 20 µL of FAMEs standards) were added and incubated for 30 min at 37ºC in a shaker. FAMES mixture was prepared in chloroform according to Kind et al (31) 31. Kind, T., Wohlgemuth, G., Lee, D. Y., Lu, Y., Palazoglu, M., Shahbaz, S., & Fiehn, O. (2009). FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Analytical chemistry, 81(24), 10038–10048. https://doi.org/10.1021/ac9019522 |
Processing Storage Conditions: | Described in summary |
Extract Storage: | -80℃ |
Sample Derivatization: | For polar analysis via GC-MS, derivatization was done. Briefly, 40 µL of methoxyaminhydrochloride (20 mg/ml in pyridine) was added to the dried sample and incubated for 2 hours at 37ºC in a shaker. After, 70 µL of N-methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) mixture (1 mL MSTFA and 20 µL of FAMEs standards) were added and incubated for 30 min at 37ºC in a shaker |
Sample Spiking: | each sample spiked with 30 microliters of 0.2 mg/mL (in water) ribitol. |
Combined analysis:
Analysis ID | AN005423 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Agilent 7200 GC-QTOF |
Column | Agilent HP5-MS (30m x 0.25mm, 0.25 um) |
MS Type | EI |
MS instrument type | GC-TOF |
MS instrument name | Agilent 7200 QTOF |
Ion Mode | POSITIVE |
Units | peak height |
Chromatography:
Chromatography ID: | CH004112 |
Chromatography Summary: | Analyses were done using a combined GC/MS instrument, 7200 GC-QTOF system (Agilent), with an HP-5MS UI column (30 m, 0.25 mm, and 0.25 mm; Agilent) and an in-house method of analysis for untargeted metabolomics. The settings included a starting temperature of 80 °C held for 2 min, increased at 15 °C per minute to 350 °C followed by a final hold for 6 min (total run time of 25 min). Ion source temperature was set to 250 °C, while the scanning mass range was set as 60 to 600 m/z. Samples were injected in random order to minimize bias. |
Instrument Name: | Agilent 7200 GC-QTOF |
Column Name: | Agilent HP5-MS (30m x 0.25mm, 0.25 um) |
Column Temperature: | 80 - 350 |
Flow Gradient: | NA |
Flow Rate: | NA |
Solvent A: | NA |
Solvent B: | NA |
Strong Wash Solvent Name: | 100% acetone |
Chromatography Type: | GC |
MS:
MS ID: | MS005149 |
Analysis ID: | AN005423 |
Instrument Name: | Agilent 7200 QTOF |
Instrument Type: | GC-TOF |
MS Type: | EI |
MS Comments: | The settings included a starting temperature of 80 °C held for 2 min, increased at 15 °C per minute to 350 °C followed by a final hold for 6 min (total run time of 25 min). Ion source temperature was set to 250 °C, while the scanning mass range was set as 60 to 600 m/z. Samples were injected in random order to minimize bias. For data processing, all raw data files were converted to .abf format using abfconverter. These files were imported into MS-DIAL v4.60 for pre-processing where the following parameters were used: Retention time range = 4-24 minutes, Mass range = 60-600 Da, Minimum peak height = 1000, Retention index tolerance (for identification based on FAMES index) = 3000, Retention time tolerance (for alignment) = 0.075 minutes. The Fiehn GCMS metabolite library was used for identification Peak heights were exported to Excel for post-processing. Metabolites that only had a quant mass of 147-149 or 70-79 were removed as these masses often represent derivatization products. Finally, signals from duplicate identified metabolites were summed as the same metabolite may have different derivatization forms but is not truly a different metabolite. NOTE: The GC and MS are a joined system. |
Ion Mode: | POSITIVE |