Summary of Study ST002783

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 PR001736. The data can be accessed directly via it's Project DOI: 10.21228/M89Q7K 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.

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Study IDST002783
Study TitleMetabolic changes of the pig kidney during isolated normothermic perfusion with autologous whole blood - perfusate
Study TypeExperimental
Study SummaryThis study investigates how glucose, lactate and 20 amino acids in the perfusate of normothermically perfused pig kidneys changes over time. It also studies how type and severity of ischemia before perfusion (cold or warm ischemia) change this profile.
Institute
KU Leuven
DepartmentMicrobiology, Immunology and Transplantation
LaboratoryLab of Abdominal Transplantation
Last NameJochmans
First NameIna
AddressHerestraat 49, Leuven, 3000, Belgium
Emailina.jochmans@kuleuven.be
PhoneNone
Submit Date2023-07-17
Num Groups3
Total Subjects18 kidneys
Num Males9 male pigs
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-08-07
Release Version1
Ina Jochmans Ina Jochmans
https://dx.doi.org/10.21228/M89Q7K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001736
Project DOI:doi: 10.21228/M89Q7K
Project Title:Metabolic changes during normothermic isolated kidney perfusion
Project Type:Experimental
Project Summary:Normothermic isolated kidney perfusion is being developed as a method to preserve donor kidneys and to assess their future function before they are transplanted. Donor kidneys can be exposed to different types and degrees of ischemic injury before they are preserved. This project studies how the metabolome changes in relation to different types and degrees of ischemia.
Institute:KU Leuven
Department:Microbiology, Immunology and Transplantation
Laboratory:Lab of Abdominal Transplantation
Last Name:Jochmans
First Name:Ina
Address:Herestraat 49, Leuven, 3000, Belgium
Email:ina.jochmans@kuleuven.be
Phone:None
Funding Source:FTBO, KOOR, FWO
Contributors:Julie De Beule, Bart Ghesquière, Ina Jochmans

Subject:

Subject ID:SU002890
Subject Type:Mammal
Subject Species:Sus scrofa
Taxonomy ID:9823
Age Or Age Range:~4 months
Weight Or Weight Range:35-45 kg
Gender:Male
Animal Animal Supplier:TOPIGS TN70, Tojapigs, the Netherlands
Animal Light Cycle:12 hours
Animal Water:ad libitum

Factors:

Subject type: Mammal; Subject species: Sus scrofa (Factor headings shown in green)

mb_sample_id local_sample_id Group Timepoint
SA29866772_T0CI 0
SA29866833_T0CI 0
SA29866971_T0CI 0
SA29867030_T0CI 0
SA29867129_T0CI 0
SA29867275_T0CI 0
SA29867371_T2CI 120
SA29867472_T2CI 120
SA29867533_T2CI 120
SA29867629_T2CI 120
SA29867775_T2CI 120
SA29867830_T2CI 120
SA29867975_T0.25CI 15
SA29868071_T0.25CI 15
SA29868130_T0.25CI 15
SA29868272_T0.25CI 15
SA29868333_T0.25CI 15
SA29868429_T0.25CI 15
SA29868572_T3CI 180
SA29868675_T3CI 180
SA29868771_T3CI 180
SA29868833_T3CI 180
SA29868929_T3CI 180
SA29869030_T3CI 180
SA29869175_T4CI 240
SA29869229_T4CI 240
SA29869371_T4CI 240
SA29869430_T4CI 240
SA29869533_T4CI 240
SA29869672_T4CI 240
SA29869772_T0.50CI 30
SA29869830_T0.50CI 30
SA29869929_T0.50CI 30
SA29870071_T0.50CI 30
SA29870133_T0.50CI 30
SA29870275_T0.50CI 30
SA29870330_T0.75CI 45
SA29870472_T0.75CI 45
SA29870533_T0.75CI 45
SA29870671_T0.75CI 45
SA29870729_T0.75CI 45
SA29870875_T0.75CI 45
SA29870933_T1CI 60
SA29871072_T1CI 60
SA29871130_T1CI 60
SA29871271_T1CI 60
SA29871375_T1CI 60
SA29871429_T1CI 60
SA29871567_T0Control 0
SA29871634_T0Control 0
SA29871719_T0Control 0
SA29871831_T0Control 0
SA29871976_T0Control 0
SA29872070_T0Control 0
SA29872131_T2Control 120
SA29872267_T2Control 120
SA29872376_T2Control 120
SA29872470_T2Control 120
SA29872519_T2Control 120
SA29872634_T2Control 120
SA29872767_T0.25Control 15
SA29872870_T0.25Control 15
SA29872976_T0.25Control 15
SA29873031_T0.25Control 15
SA29873119_T0.25Control 15
SA29873234_T0.25Control 15
SA29873334_T3Control 180
SA29873419_T3Control 180
SA29873531_T3Control 180
SA29873676_T3Control 180
SA29873767_T3Control 180
SA29873870_T3Control 180
SA29873919_T4Control 240
SA29874070_T4Control 240
SA29874134_T4Control 240
SA29874276_T4Control 240
SA29874367_T4Control 240
SA29874431_T4Control 240
SA29874531_T0.50Control 30
SA29874676_T0.50Control 30
SA29874767_T0.50Control 30
SA29874870_T0.50Control 30
SA29874919_T0.50Control 30
SA29875034_T0.50Control 30
SA29875131_T0.75Control 45
SA29875219_T0.75Control 45
SA29875370_T0.75Control 45
SA29875476_T0.75Control 45
SA29875567_T0.75Control 45
SA29875634_T0.75Control 45
SA29875731_T1Control 60
SA29875870_T1Control 60
SA29875976_T1Control 60
SA29876067_T1Control 60
SA29876134_T1Control 60
SA29876219_T1Control 60
SA29876368_T0WI 0
SA29876469_T0WI 0
SA29876532_T0WI 0
SA29876673_T0WI 0
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Collection:

Collection ID:CO002883
Collection Summary:Perfusate samples were collected in ethylenediaminetetraacetic acid (EDTA) tubes, at baseline (before the kidney was mounted on the normothermic perfusion device), every 15 minutes during the first hour and hourly thereafter. One milliliter perfusate aliquots (centrifuged 1000g, 10 minutes, 4°C) were snap frozen in liquid nitrogen and stored at -80°C until analysis.
Sample Type:Perfusate
Collection Frequency:Baseline (T0) and during perfusion at 15 min (T0.25), 30 min (T0.50), 45 min (T0.75), 1 hour (T1), 2 hours (T2), 3 hours (T3), 4 hours (T4)
Storage Conditions:-80℃
Additives:EDTA

Treatment:

Treatment ID:TR002899
Treatment Summary:Three experimental conditions were investigated (n=6/group): (a) Controls; (b) warm ischemia (WI) simulating hypoxic acute kidney injury; (c) cold ischemia (CI) replicating clinical cold storage. Control kidneys were retrieved, flushed with cold IGL-1, and immediately reperfused. CI group, kidneys were exposed to 22h of CI by submerging them in IGL- 1 (a clinical preservation solution for cold storage) and storing them on ice. In WI, the renal artery and vein were clamped for 60 min before retrieval. In the All kidneys were flushed with 200 ml of Ringer’s solution before mounting them on the ex situ circuit to wash out IGL-1.
Animal Anesthesia:Pigs were sedated by an intramuscular injection of Tiletamine/Zolazepam (8 mg/kg, Zoletil®, Virbac, Belgium) and Xylazine (2 mg/kg, Xylazine®, VMD pharma, Belgium) to allow orotracheal intubation. Anesthesia was maintained by inhalation of isoflurane (1% Isovet®, Piramal Critical Care B.V., Belgium) and continuous infusion of fentanyl (8 µg/kg, Fentanyl®, Janssen Pharmaceutica, Belgium).
Animal Acclimation Duration:Minimum of 2 days
Animal Fasting:Overnight
Animal Endp Euthanasia:Non-recovery study

Sample Preparation:

Sampleprep ID:SP002896
Sampleprep Summary:Samples were extracted in an 80% methanol (80:20 methanol:water) (Methanol ≥99.9%, HiPerSolv CHROMANORM®, ULTRA for LC-MS, suitable for UPLC/UHPLC-MS instruments, VWR, Belgium) extraction buffer containing 1 µM of deuterated D27 myristic acid, 5 µM D12 glucose, 3 µM 13C5-D5-15N Glutamic acid and 3 µM D7-15N4-Arginine as internal standards. 10 µl of sample was added to 990 µl of the extraction buffer and stored overnight at -80 °C. Insolubilities and precipitated proteins were removed by centrifugation at 20.000 g, for 15 min at 4 °C. 200 µL of the supernatant was transferred to an appropriate mass-spectrometry vial. 10 µl of sample was added to 990 µl of the extraction buffer and stored overnight at -80 °C.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004530
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1290 Infinity
Column Agilent InfinityLab Poroshell 120 (2.1 x 150 mm, 2.7 um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Focus
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH003403
Chromatography Summary:10 µl was loaded onto an Ultra Performance Liquid Chromatograph (UPLC) equipped with a Hydrophilic Interaction Liquid Chromatography (HILIC) column (InfinityLab Poroshell 120 HILIC-Z PEEK-lined 2.1 x 150 mm, 2.7 µm column; Agilent, Santa Clara, USA)) and connected in-line to a Q-exactive Orbitrap Focus (Thermo Fisher Scientific, Massachusetts, USA) mass spectrometer. A linear gradient was built up starting with 90% solvent A (LC-MS grade acetonitrile, Acetonitrile hypergrade for LC-MS LiChrosolv, Supelco (Merck), Germany) and 10% solvent B (10 mM ammonium acetate (LiChropur™, eluent additive for LC-MS, (Merck), Germany), pH 9.3). At 2 min the gradient increased to 60% of solvent B and maintained at 60% until 15 min. The gradient returned to 10% solvent B at 16 min and remained until 25 min. The flow rate was 250 µl/min and the column was kept at 25°C throughout the analysis. The MS operated in negative ion mode, with a spray voltage of 2.9 kV and a temperature of the capillary of 325 °C. Gas settings were as follows: sheath gas 40 and auxiliary gas 15. The vaporizer temperature was set at 300 °C. A full scan (resolution of 70.000 and scan range of m/z 70-1050) was applied. XCalibur version to operate the LC-MS was 4.2.47.
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent InfinityLab Poroshell 120 (2.1 x 150 mm, 2.7 um)
Column Temperature:25°C
Flow Gradient:A linear gradient was built up starting with 90% solvent A and 10% solvent B. At 2 min the gradient increased to 60% of solvent B and maintained at 60% until 15 min.
Flow Rate:250 µl/min
Solvent A:100% acetonitrile
Solvent B:100% water; 10 mM ammonium acetate, pH 9.3
Chromatography Type:HILIC

MS:

MS ID:MS004277
Analysis ID:AN004530
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw MS data were converted into mzML using the MSConvert tool of Proteowizard (version 3.0.20247). Peak picking was performed with El_Maven (El_Maven, Elucidata, Massachusetts, USA, version 0.12.0). Metabolites were identified using an in-house library containing exact mass and retention time. The mass accuracy during data processing in El Maven was set at 10 ppm. Calculation of abundances was done in the LC-MS Workflow of El_Maven. Raw abundances (peak area values) for each metabolite were corrected for internal standard (Myristic acid d27).
Ion Mode:NEGATIVE
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