Summary of Study ST003338

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 PR002075. The data can be accessed directly via it's Project DOI: 10.21228/M8D824 This work is supported by NIH grant, U2C- DK119886.

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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 IDST003338
Study TitleGRATEFUL (Graft Temperature Evaluation during Lung transplantation) - metabolomics
Study SummaryWe aimed to characterize the rewarming ischemia phase during LuTx by measuring organ temperature and comparing metabolome profiles in tissue obtained at the end versus the start of implantation.
Institute
KU Leuven
Last NameVan Slambrouck
First NameJan
AddressHerestraat 49, Leuven, Vlaams-Brabant, 3000, Belgium
Emailjan.vanslambrouck@kuleuven.be
Phone+32 16 19 46 17
Submit Date2024-05-30
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-08-12
Release Version1
Jan Van Slambrouck Jan Van Slambrouck
https://dx.doi.org/10.21228/M8D824
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002075
Project DOI:doi: 10.21228/M8D824
Project Title:The effect of rewarming ischemia on tissue transcriptome and metabolome signatures: a clinical observational study in lung transplantation
Project Type:Clinical observational study in lung transplantation
Project Summary:BACKGROUND: In lung transplantation (LuTx), various ischemic phases exist, yet the rewarming ischemia time (RIT) during implantation has often been overlooked. During RIT, lungs are deflated and exposed to the body temperature in the recipient's chest cavity. Our prior clinical findings demonstrated that prolonged RIT increases the risk of primary graft dysfunction. However, the molecular mechanisms of rewarming ischemic injury in this context remain unexplored. We aimed to characterize the rewarming ischemia phase during LuTx by measuring organ temperature and comparing transcriptome and metabolome profiles in tissue obtained at the end versus the start of implantation. METHODS: In a clinical observational study, 34 double-LuTx with ice preservation were analyzed. Lung core and surface temperature (n=65 and 55 lungs) was measured during implantation. Biopsies (n=59 lungs) were wedged from right middle lobe and left lingula at start and end of implantation. Tissue transcriptomic and metabolomic profiling were performed. RESULTS: Temperature increased rapidly during implantation, reaching core/surface temperatures of 21.5°C/25.4°C within 30min. Transcriptomics showed increased pro-inflammatory signaling and oxidative stress at the end of implantation. Upregulation of NLRP3 and NFKB1 correlated with RIT. Metabolomics indicated elevated levels of amino acids, hypoxanthine, uric acid, cysteineglutathione disulfide alongside decreased levels of glucose and carnitines. Arginine, tyrosine, and 1-carboxyethylleucine showed correlation with incremental RIT. CONCLUSIONS: The final rewarming ischemia phase in LuTx involves rapid organ rewarming, accompanied by transcriptomic and metabolomic changes indicating pro-inflammatory signaling and disturbed cell metabolism. Limiting implantation time and lung cooling represent potential interventions to alleviate rewarming ischemic injury.
Institute:KU Leuven
Laboratory:Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE)
Last Name:Ceulemans
First Name:Laurens
Address:Herestraat 49, Leuven, Vlaams-Brabant, 3000, Belgium
Email:laurens.ceulemans@uzleuven.be
Phone:+32 16 34 34 25

Subject:

Subject ID:SU003459
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Rewarming ischemia time in min
SA362719MCF001777_JV117_10Lung 100
SA362720MCF001777_JV118_8Lung 100
SA362721MCF001777_JV118_7Lung 100
SA362722MCF001777_JV118_5Lung 100
SA362723MCF001777_JV117_9Lung 100
SA362724MCF001777_JV117_8Lung 100
SA362725MCF001777_JV117_7Lung 100
SA362726MCF001777_JV117_4Lung 100
SA362727MCF001777_JV118_3Lung 100
SA362728MCF001777_JV118_2Lung 100
SA362729MCF001777_JV118_1Lung 100
SA362730MCF001777_JV117_11Lung 100
SA362731MCF001777_JV118_6Lung 100
SA362732MCF001777_JV117_3Lung 100
SA362733MCF001777_JV117_2Lung 100
SA362734MCF001777_JV117_1Lung 100
SA362735MCF001777_JV117_5Lung 100
SA362736MCF001777_JV117_6Lung 100
SA362737MCF001777_JV118_4Lung 100
SA362738MCF001777_JV117_12Lung 100
SA362739MCF001777_JV118_10Lung 100
SA362740MCF001777_JV118_11Lung 100
SA362741MCF001777_JV118_12Lung 100
SA362742MCF001777_JV118_9Lung 100
SA362743MCF001777_JV14_9Lung 101
SA362744MCF001777_JV14_6Lung 101
SA362745MCF001777_JV14_5Lung 101
SA362746MCF001777_JV13_5Lung 101
SA362747MCF001777_JV13_6Lung 101
SA362748MCF001777_JV14_4Lung 101
SA362749MCF001777_JV14_2Lung 101
SA362750MCF001777_JV14_8Lung 101
SA362751MCF001777_JV14_7Lung 101
SA362752MCF001777_JV13_9Lung 101
SA362753MCF001777_JV13_8Lung 101
SA362754MCF001777_JV13_7Lung 101
SA362755MCF001777_JV14_3Lung 101
SA362756MCF001777_JV13_4Lung 101
SA362757MCF001777_JV14_1Lung 101
SA362758MCF001777_JV13_10Lung 101
SA362759MCF001777_JV13_2Lung 101
SA362760MCF001777_JV13_1Lung 101
SA362761MCF001777_JV14_12Lung 101
SA362762MCF001777_JV14_11Lung 101
SA362763MCF001777_JV14_10Lung 101
SA362764MCF001777_JV13_12Lung 101
SA362765MCF001777_JV13_11Lung 101
SA362766MCF001777_JV13_3Lung 101
SA362767MCF001777_JV08_10Lung 105
SA362768MCF001777_JV08_12Lung 105
SA362769MCF001777_JV08_11Lung 105
SA362770MCF001777_JV07_8Lung 105
SA362771MCF001777_JV07_12Lung 105
SA362772MCF001777_JV07_11Lung 105
SA362773MCF001777_JV07_10Lung 105
SA362774MCF001777_JV08_7Lung 105
SA362775MCF001777_JV07_9Lung 105
SA362776MCF001777_JV07_7Lung 105
SA362777MCF001777_JV08_8Lung 105
SA362778MCF001777_JV08_6Lung 105
SA362779MCF001777_JV07_4Lung 105
SA362780MCF001777_JV07_1Lung 105
SA362781MCF001777_JV07_2Lung 105
SA362782MCF001777_JV07_3Lung 105
SA362783MCF001777_JV08_1Lung 105
SA362784MCF001777_JV08_2Lung 105
SA362785MCF001777_JV08_3Lung 105
SA362786MCF001777_JV08_9Lung 105
SA362787MCF001777_JV07_6Lung 105
SA362788MCF001777_JV08_4Lung 105
SA362789MCF001777_JV08_5Lung 105
SA362790MCF001777_JV07_5Lung 105
SA362791MCF001777_JV52_2Lung 106
SA362792MCF001777_JV51_8Lung 106
SA362793MCF001777_JV52_4Lung 106
SA362794MCF001777_JV52_5Lung 106
SA362795MCF001777_JV52_6Lung 106
SA362796MCF001777_JV51_4Lung 106
SA362797MCF001777_JV51_5Lung 106
SA362798MCF001777_JV51_10Lung 106
SA362799MCF001777_JV51_11Lung 106
SA362800MCF001777_JV52_1Lung 106
SA362801MCF001777_JV52_10Lung 106
SA362802MCF001777_JV52_11Lung 106
SA362803MCF001777_JV52_12Lung 106
SA362804MCF001777_JV51_7Lung 106
SA362805MCF001777_JV51_12Lung 106
SA362806MCF001777_JV51_9Lung 106
SA362807MCF001777_JV52_7Lung 106
SA362808MCF001777_JV51_3Lung 106
SA362809MCF001777_JV51_2Lung 106
SA362810MCF001777_JV51_1Lung 106
SA362811MCF001777_JV52_3Lung 106
SA362812MCF001777_JV51_6Lung 106
SA362813MCF001777_JV52_8Lung 106
SA362814MCF001777_JV52_9Lung 106
SA362815MCF001777_JV49_9Lung 107
SA362816MCF001777_JV50_9Lung 107
SA362817MCF001777_JV50_8Lung 107
SA362818MCF001777_JV50_3Lung 107
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Collection:

Collection ID:CO003452
Collection Summary:A peripheral wedge biopsy from the right middle lobe and left upper lobe lingula was obtained at start and end of implantation, before reperfusion. From each biopsy, a piece was immediately frozen on dry ice for subsequent metabolite extraction.
Collection Protocol ID:GraTEfuL
Collection Protocol Filename:Graft Temperature Evaluation during Lung transplantation
Collection Protocol Comments:S67052 approved by UZ/KU Leuven Ethics Committee
Sample Type:Lung
Collection Method:Peripheral wedge biopsy donor lung tissue
Collection Location:Right middle lobe and lingula of left upper lobe
Collection Frequency:2 time points: start and end of implantation, before organ reperfusion
Storage Conditions:-80℃
Collection Vials:cryotube
Storage Vials:cryotube
Collection Tube Temp:not specified, stored on dry ice
Additives:none

Treatment:

Treatment ID:TR003468
Treatment Summary:No treatment. This project was a clinical observational study.

Sample Preparation:

Sampleprep ID:SP003466
Sampleprep Summary:Tissue samples were stored at -80°C from delivery to the start of the sample preparation. Tissues were weighed and transferred to a homogenization tube containing 1.4 mm ceramic beads. To these tubes 800 uL of extraction buffer (composed of 80% methanol in H2O) was added. The samples were then homogenized for two times 30 seconds at 6500 rpm using the Precellys 24 (Bertin Instruments, France). This homogenate was kept overnight at -80 degrees C to precipitate the present proteins. On this methanol extract, a liquid-liquid extraction method was employed to fractionate the samples. The methanol extraction was centrifuged at 17.000 xg for 10 minutes, after which 400 uL of the supernatant was transferred to a fresh Eppendorf tube.To this, 400 uL of chloroform was added, followed by thorough vortexing for 60 seconds to achieve an optimal extraction. An additional 130 uL of H2O was then introduced to induce phase separation, followed by another brief vortexing period of 15 seconds. This mixture was then subjected to centrifugation for 5 minutes at 5.000 xg. Hereafter, 200 uL of the upper polar phase was transferred to an MS vial, while an equal volume of the lower apolar phase was dried using a CentriVap system(Labconco, USA). The resulting dried pellet was then reconstituted in 100% methanol, before being transferred to an MS vial. Lastly, for both phases a QC sample was made by pooling together 10 uL of each sample.

Combined analysis:

Analysis ID AN005470 AN005471
Analysis type MS MS
Chromatography type None (Direct infusion) None (Direct infusion)
Chromatography system none none
Column none none
MS Type ESI ESI
MS instrument type FT-ICR FT-ICR
MS instrument name Bruker scimaX MRMS Bruker scimaX MRMS
Ion Mode POSITIVE NEGATIVE
Units relative intensity relative intensity

Chromatography:

Chromatography ID:CH004155
Instrument Name:none
Column Name:none
Column Temperature:none
Flow Gradient:none
Flow Rate:none
Solvent A:none
Solvent B:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS005196
Analysis ID:AN005470
Instrument Name:Bruker scimaX MRMS
Instrument Type:FT-ICR
MS Type:ESI
MS Comments:Mass Spectrometry measurements were performed using an Infinity ll autosampler and pump System (Agilent, USA) coupled to a ScimaX 7T Magnetic Resonance Mass Spectrometer (Bruker, USA) operated in positive mode and in technical replicates.Data collection was performed using the ftmsControl and HyStar software (Bruker, USA). The initial data analyses were performed by MetaboScape 2022b (Bruker, USA). This software performs peak picking, feature detection and feature annotation using exact mass and isotope configuration. The human metabolome database (HMDB) was used as the database for feature annotation.
Ion Mode:POSITIVE
  
MS ID:MS005197
Analysis ID:AN005471
Instrument Name:Bruker scimaX MRMS
Instrument Type:FT-ICR
MS Type:ESI
MS Comments:Mass Spectrometry measurements were performed using an Infinity ll autosampler and pump System (Agilent, USA) coupled to a ScimaX 7T Magnetic Resonance Mass Spectrometer (Bruker, USA) operated in negative mode and in technical replicates.Data collection was performed using the ftmsControl and HyStar software (Bruker, USA). The initial data analyses were performed by MetaboScape 2022b (Bruker, USA). This software performs peak picking, feature detection and feature annotation using exact mass and isotope configuration. The human metabolome database (HMDB) was used as the database for feature annotation.
Ion Mode:NEGATIVE
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