Summary of Study ST003518

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 PR002163. The data can be accessed directly via it's Project DOI: 10.21228/M81J94 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST003518
Study TitleWheat-based protein slows cyst growth in Pkd1 knockout mice
Study TypeUntargeted Metabolomics MS with MSMS annotations
Study SummaryPkd1KO vs Wild Type mice supplemented with diet enriched with either Glutamine or Lysine versus Vehicle. Profiling potential metabolic changes via high resolution LC-MS/MS mass spectrometry.
Institute
University of Alabama, Birmingham
DepartmentDivision of Nephrology, Department of Medicine
LaboratoryTakamitsu Saigusa
Last NameSaigusa
First NameTakamitsu
AddressMcCallum Basic Health Science Building, Room 533, 1918 University Blvd. Birmingham, AL 35233
Emailtsaigusa@uabmc.edu
Phone(205)975-2021
Submit Date2024-10-11
Num Groups6
Total Subjects30
Num Males15
Num Females15
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2026-01-12
Release Version1
Takamitsu Saigusa Takamitsu Saigusa
https://dx.doi.org/10.21228/M81J94
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002163
Project DOI:doi: 10.21228/M81J94
Project Title:Wheat-based protein slows cyst growth in Pkd1 knockout mice
Project Type:Untargeted Metabolomics
Project Summary:Abstract: Dietary load and composition are known contributors that accelerate cyst growth in polycystic kidney disease (PKD). High protein intake, which increases amino acid burden in the kidneys, is one such factor. Despite identical protein load, a plant-based wheat-gluten (WG) diet was recently reported to blunt the inflammatory response of animal-based casein diet in a hypertensive model. Considering the importance of pro-inflammatory signals on cystogenesis in PKD, we therefore sought to determine whether a WG compared to casein diet would decelerate cyst progression. Tamoxifen-inducible, global Pkd1 knockout (Pkd1KO) mice were fed either a low casein (6%), high casein (60%), or high wheat-gluten (60%) protein diet for 6 weeks. In a separate cohort, mice were gavaged daily with vehicle, lysine, or glutamine for 4 weeks while maintained on a normal protein (18%) diet. Tissues were used for histology, flow cytometry, mitochondrial function, metabolomics, and various biochemical assays. WG-fed mice had reduced kidney macrophage percentages, proinflammatory cytokine expression, and cyst growth compared to casein-fed mice. Protein source did not alter kidney mitochondria function. Supplementation with lysine, the highest amino acid in casein versus WG diet, increased kidney cyst growth, acid production, and metabolic disarray. This did not occur with glutamine supplementation, the highest amino acid in WG versus casein diet. Neither supplementation mounted an inflammatory response. A plant-based, low-lysine diet slows disease burden in a murine model of PKD. This easily modifiable diet may be a beneficial intervention for PKD patients.
Institute:University of Alabama at Birmingham
Department:Division of Nephrology, Department of Medicine
Last Name:Saigusa
First Name:Takamitsu
Address:McCallum Basic Health Science Building, Room 533, 1918 University Blvd. Birmingham, AL 35233
Email:tsaigusa@uabmc.edu
Phone:2059343462
Funding Source:NIDDK
Contributors:Randee Sedaka, Jifeng Huang, Shinobu Yamaguchi, Emily Hallit, Aida Moran-Reyna, Jung-Shan Hsu, Caleb Lovelady, Ayaka Fujihashi, Mohammad Sako, Malgorzata Kasztan, Gloria Benavides , Landon Wilson, Victor Darley-Usmar, Stephen Barnes

Subject:

Subject ID:SU003647
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:6 weeks
Gender:Male and female
Animal Light Cycle:12:12 light-dark cycle
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Genotype Treatment
SA386446NEG_5539Pkd1KO Glutamine
SA386447POS_5538Pkd1KO Glutamine
SA386448POS_5539Pkd1KO Glutamine
SA386449NEG_6592Pkd1KO Glutamine
SA386450NEG_8651Pkd1KO Glutamine
SA386451NEG_11427Pkd1KO Glutamine
SA386452NEG_11426Pkd1KO Glutamine
SA386453NEG_8659Pkd1KO Glutamine
SA386454NEG_8846Pkd1KO Glutamine
SA386455NEG_5851Pkd1KO Glutamine
SA386456NEG_5831Pkd1KO Glutamine
SA386457NEG_5538Pkd1KO Glutamine
SA386458POS_8659Pkd1KO Glutamine
SA386459POS_11427Pkd1KO Glutamine
SA386460POS_6592Pkd1KO Glutamine
SA386461POS_5831Pkd1KO Glutamine
SA386462POS_5851Pkd1KO Glutamine
SA386463POS_8846Pkd1KO Glutamine
SA386464POS_8651Pkd1KO Glutamine
SA386465POS_11426Pkd1KO Glutamine
SA386466POS_5704Pkd1KO Lysine
SA386467POS_5705Pkd1KO Lysine
SA386468POS_6594Pkd1KO Lysine
SA386469POS_5525Pkd1KO Lysine
SA386470POS_5724Pkd1KO Lysine
SA386471POS_5710Pkd1KO Lysine
SA386472POS_6574Pkd1KO Lysine
SA386473POS_11469Pkd1KO Lysine
SA386474NEG_5705Pkd1KO Lysine
SA386475NEG_6594Pkd1KO Lysine
SA386476NEG_5531Pkd1KO Lysine
SA386477NEG_5702Pkd1KO Lysine
SA386478NEG_5704Pkd1KO Lysine
SA386479POS_5702Pkd1KO Lysine
SA386480NEG_11469Pkd1KO Lysine
SA386481NEG_6574Pkd1KO Lysine
SA386482NEG_5710Pkd1KO Lysine
SA386483NEG_5724Pkd1KO Lysine
SA386484NEG_5525Pkd1KO Lysine
SA386485POS_5531Pkd1KO Lysine
SA386486NEG_5698Pkd1KO Vehicle
SA386487POS_6571Pkd1KO Vehicle
SA386488NEG_6571Pkd1KO Vehicle
SA386489NEG_5533Pkd1KO Vehicle
SA386490NEG_5836Pkd1KO Vehicle
SA386491NEG_8847Pkd1KO Vehicle
SA386492NEG_5523Pkd1KO Vehicle
SA386493NEG_5537Pkd1KO Vehicle
SA386494NEG_5534Pkd1KO Vehicle
SA386495NEG_5524Pkd1KO Vehicle
SA386496NEG_5532Pkd1KO Vehicle
SA386497POS_5524Pkd1KO Vehicle
SA386498POS_5532Pkd1KO Vehicle
SA386499POS_5533Pkd1KO Vehicle
SA386500POS_5836Pkd1KO Vehicle
SA386501POS_8847Pkd1KO Vehicle
SA386502POS_5523Pkd1KO Vehicle
SA386503POS_5537Pkd1KO Vehicle
SA386504POS_5534Pkd1KO Vehicle
SA386505POS_5698Pkd1KO Vehicle
Showing results 1 to 60 of 60

Collection:

Collection ID:CO003640
Collection Summary:Kidneys cortex tissue (100 mg) was bead-homogenized, then extracted using the Bligh-Dyer chloroform: methanol procedure.
Sample Type:Kidney cortex
Storage Conditions:-80℃
Collection Vials:2.0 mL Microcentrifuge tubes
Storage Vials:2.0 mL Microcentrifuge tubes
Collection Tube Temp:-196℃
Additives:None

Treatment:

Treatment ID:TR003656
Treatment Summary:Two weeks after tamoxifen induction, mice were randomly assigned to consume a low casein (6%; TD.90016), high casein (60%; TD.6220), or high wheat-gluten (WG; 60%; TD.190147) protein diet for 6 weeks ad libitum. All diets were formulated by Envigo (Indianapolis, IN) to be isocaloric (3.7 kcal/g). Nutritional and amino acid composition of each diet are shown in Supplementary Table 1 & 2, respectively. In a separate cohort, mice received an oral gavage (OG) of glutamine (5.25 g/kg/day; G8540, MilliporeSigma, Burlington, MA), lysine (6.8 g/kg/day; L8662, MilliporeSigma), or vehicle (1X phosphate-buffered saline; PBS) for 4 weeks while maintained on normal protein (18%) chow.

Sample Preparation:

Sampleprep ID:SP003654
Sampleprep Summary:Kidneys cortex tissue (100 mg) was bead-homogenized, then extracted using the Bligh-Dyer chloroform: methanol procedure. Briefly, the upper aqueous layer was transferred to a clean glass tube with cold methanol (80%) to further remove proteins. After centrifugation, supernatants were dried and re-suspended in 0.1% formic acid.
Sampleprep Protocol ID:Bligh-Dyer Extraction plus 80% Methanol Extraction
Sampleprep Protocol Filename:Metabolomics_Writeup_LCMS_ExionSystem_092824_Saigusa_edits
Sampleprep Protocol Comments:Bligh-Dyer extraction with additional 80% cold aqueous methanol extraction for additional protein precipitation step.
Processing Storage Conditions:4℃
Extraction Method:Bligh-Dyer Protocol
Extract Storage:-80℃
Sample Resuspension:200 μL of 0.1% Formic acid
Sample Derivatization:none
Sample Spiking:none
Subcellular Location:N/A

Combined analysis:

Analysis ID AN005775 AN005776
Chromatography ID CH004383 CH004383
MS ID MS005495 MS005496
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system EXION UPLC EXION UPLC
Column Phenomenex Luna Omega Polar C18 (100 x 2.1 mm, 1.6 um) Phenomenex Luna Omega Polar C18 (100 x 2.1 mm, 1.6 um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name ABI Sciex 5600+ TripleTOF ABI Sciex 5600+ TripleTOF
Ion Mode POSITIVE NEGATIVE
Units intensity intensity

Chromatography:

Chromatography ID:CH004383
Chromatography Summary:C18 Reverse Phase UPLC-MS
Chromatography Comments:Calibration Standard analyzed every 5 injections
Instrument Name:EXION UPLC
Column Name:Phenomenex Luna Omega Polar C18 (100 x 2.1 mm, 1.6 um)
Column Temperature:40℃
Flow Gradient:2-50% B over 5 minutes
Flow Rate:500 μL/min
Injection Temperature:4℃
Internal Standard:none
Sample Injection:10 μL
Solvent A:100% Double-distilled Water; 0.1% Formic acid
Solvent B:100% Acetonitrile; 0.1% Formic acid
Analytical Time:10 min
Capillary Voltage:5500/4500V (+/-) ionization
Oven Temperature:40C
Preconditioning:1 minute equilibration time
Weak Wash Solvent Name:ddH20
Weak Wash Volume:50 μL
Strong Wash Solvent Name:Methanol
Strong Wash Volume:20 μL
Target Sample Temperature:40℃
Sample Loop Size:100 μL
Sample Syringe Size:100 μL
Randomization Order:yes
Chromatography Type:Reversed phase

MS:

MS ID:MS005495
Analysis ID:AN005775
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:For each specimen analyzed, an aliquot (10 μL) of each sample was loaded onto a Phenomenex 2.1 x 100 mm, 1.6 μm Luna Omega, 80 Å reverse-phase column (Torrance, CA). After equilibration with 0.1% formic acid, each sample was subjected to a linear gradient of 2-50% mobile phase B for 5 min, 50-98% B until 6.0 min with a 1-minute hold, and then re-equilibration at initial conditions for 3 minutes using an Exion UHPLC (Sciex, Toronto, Ontario) and a flow rate of 500 μL/min. The mobile phases were A) ddH2O with 0.1% formic acid and B) acetonitrile with 0.1% formic acid, respectively. The SCIEX 5600 Triple-TOF mass spectrometer (SCIEX, Toronto, Canada) was used to analyze the metabolite profile. The IonSpray voltages for positive and negative modes were +5500/-4500 V, respectively, and the de-clustering potential was +/- 80 V. Ionspray GS1/GS2 and curtain gases were set at 40 psi and 25 psi, respectively. The interface heater temperature was 400℃. Eluted compounds were subjected to a time-of-flight survey scan from m/z 50-1000 only. Pooled samples containing equal volumes from each biological specimen was created to analyze for metabolite identifications and instrument stability. The 5600 Triple-TOF mass spectrometer conditions were identical to the analyzed plasma/sera specimens except for the addition of data-dependent scans to determine the top eight most intense ions for MSMS analysis. Product ion time-of-flight scans to obtain the tandem mass spectra of the selected parent ion(s) over the range from m/z 50-1000 were collected over 50 msec intervals using a collision energy spread of 15 eV with a set collision point of 35 eV. Spectra were centroided and de-isotoped by Analyst software, version 1.81 TF (Sciex, Toronto, Canada).
Ion Mode:POSITIVE
Collision Energy:35V
Collision Gas:CAD7
Dry Gas Flow:GS1/GS2: 40PSI
Fragmentation Method:Collision Induced Dissociation
Ion Source Temperature:400C
Ion Spray Voltage:5500
Ionization:Positive ESI
Mass Accuracy:5 ppm
Desolvation Gas Flow:40 PSI
  
MS ID:MS005496
Analysis ID:AN005776
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:For each specimen analyzed, an aliquot (10 μL) of each sample was loaded onto a Phenomenex 2.1 x 100 mm, 1.6 μm Luna Omega, 80 Å reverse-phase column (Torrance, CA). After equilibration with 0.1% formic acid, each sample was subjected to a linear gradient of 2-50% mobile phase B for 5 min, 50-98% B until 6.0 min with a 1-minute hold, and then re-equilibration at initial conditions for 3 minutes using an Exion UHPLC (Sciex, Toronto, Ontario) and a flow rate of 500 μL/min. The mobile phases were A) ddH2O with 0.1% formic acid and B) acetonitrile with 0.1% formic acid, respectively. The SCIEX 5600 Triple-TOF mass spectrometer (SCIEX, Toronto, Canada) was used to analyze the metabolite profile. The IonSpray voltages for positive and negative modes were +5500/-4500 V, respectively, and the de-clustering potential was +/- 80 V. Ionspray GS1/GS2 and curtain gases were set at 40 psi and 25 psi, respectively. The interface heater temperature was 400℃. Eluted compounds were subjected to a time-of-flight survey scan from m/z 50-1000 only. Pooled samples containing equal volumes from each biological specimen was created to analyze for metabolite identifications and instrument stability. The 5600 Triple-TOF mass spectrometer conditions were identical to the analyzed plasma/sera specimens except for the addition of data-dependent scans to determine the top eight most intense ions for MSMS analysis. Product ion time-of-flight scans to obtain the tandem mass spectra of the selected parent ion(s) over the range from m/z 50-1000 were collected over 50 msec intervals using a collision energy spread of 15 eV with a set collision point of 35 eV. Spectra were centroided and de-isotoped by Analyst software, version 1.81 TF (Sciex, Toronto, Canada).
Ion Mode:NEGATIVE
Collision Energy:35V
Collision Gas:CAD7
Dry Gas Flow:GS1/GS2: 40PSI
Fragmentation Method:Collision Induced Dissociation
Ion Source Temperature:400℃
Ion Spray Voltage:4500
Ionization:Negative ESI
Mass Accuracy:5 ppm
Desolvation Gas Flow:40 PSI
  logo