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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003311
Study TitleComplementary 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 SummaryAugmentations 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 NameAlicia
First NameJohnson
Address433 Bolivar Street New Orleans, LA 70112
Emailjadameclab@gmail.com
Phone(504) 568-1610
Submit Date2024-06-19
Num Groups4
Total Subjects24
Study CommentsRaw metabolite values (with no processing) have been given.
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2024-12-19
Release Version1
Johnson Alicia Johnson Alicia
https://dx.doi.org/10.21228/M8G533
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA358875sampleblk3blank NA NA
SA358876sampleblk2blank NA NA
SA358877sampleblk1blank NA NA
SA358878ctrl_F2brain tissue ERD No Seizure
SA358879ctrl_F1brain tissue ERD No Seizure
SA358880ctrl_M1brain tissue ERD No Seizure
SA358881ctrl_F3brain tissue ERD No Seizure
SA358882ctrl_M3brain tissue ERD No Seizure
SA358883ctrl_M2brain tissue ERD No Seizure
SA358884XO-_KA+_M3brain tissue ERD Seizure
SA358885XO-_KA+_M2brain tissue ERD Seizure
SA358886XO-_KA+_M1brain tissue ERD Seizure
SA358887XO-_KA+_F3brain tissue ERD Seizure
SA358888XO-_KA+_F2brain tissue ERD Seizure
SA358889XO-_KA+_F1brain tissue ERD Seizure
SA358890XO+_KA-_M3brain tissue ERS No Seizure
SA358891XO+_KA-_M2brain tissue ERS No Seizure
SA358892XO+_KA-_M1brain tissue ERS No Seizure
SA358893XO+_KA-_F3brain tissue ERS No Seizure
SA358894XO+_KA-_F2brain tissue ERS No Seizure
SA358895XO+_KA-_F1brain tissue ERS No Seizure
SA358896plus_F1brain tissue ERS Seizure
SA358897plus_M3brain tissue ERS Seizure
SA358898plus_F2brain tissue ERS Seizure
SA358899plus_M2brain tissue ERS Seizure
SA358900plus_M1brain tissue ERS Seizure
SA358901plus_F3brain tissue ERS Seizure
SA358902QC4pooled quality control NA NA
SA358903QC2pooled quality control NA NA
SA358904QC1pooled quality control NA NA
SA358905PreQC2pooled quality control NA NA
SA358906PreQC1pooled quality control NA NA
SA358907PostQC1pooled quality control NA NA
SA358908Post QC2pooled quality control NA NA
SA358909QC3pooled 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
  logo