Summary of Study ST000413
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 PR000322. The data can be accessed directly via it's Project DOI: 10.21228/M8V312 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000413 |
| Study Title | Metabolic profiling during ex vivo machine perfusion of the human liver (part III) |
| Study Summary | As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2016-07-01 |
| Study Comments | The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform. |
| Publications | doi:10.1038/srep22415 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-09-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000322 |
| Project DOI: | doi: 10.21228/M8V312 |
| Project Title: | Metabolic profiling during ex vivo machine perfusion of the human liver |
| Project Summary: | As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | NIH U24DK097154 |
Subject:
| Subject ID: | SU000434 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Collection Time |
|---|---|---|
| SA020296 | Inj02_SA14_BruinCSH.d | - |
| SA020297 | Inj11_SA15_BruinCSH.d | - |
| SA020298 | Inj09_SA01_BruinCSH.d | - |
| SA020299 | Inj04_SA13_BruinCSH.d | - |
| SA020300 | Inj22_SA02_BruinCSH.d | - |
| SA020301 | Inj14_SA03_BruinCSH.d | - |
| SA020302 | Inj06_SA04_BruinCSH.d | 1 Hr |
| SA020303 | Inj20_SA06_BruinCSH.d | 1 Hr |
| SA020304 | Inj23_SA17_BruinCSH.d | 1 Hr |
| SA020305 | Inj03_SA18_BruinCSH.d | 1 Hr |
| SA020306 | Inj10_SA05_BruinCSH.d | 1 Hr |
| SA020307 | Inj15_SA16_BruinCSH.d | 1 Hr |
| SA020308 | Inj08_SA20_BruinCSH.d | 2 Hr |
| SA020309 | Inj19_SA21_BruinCSH.d | 2 Hr |
| SA020310 | Inj01_SA07_BruinCSH.d | 2 Hr |
| SA020311 | Inj17_SA09_BruinCSH.d | 2 Hr |
| SA020312 | Inj13_SA19_BruinCSH.d | 2 Hr |
| SA020313 | Inj05_SA08_BruinCSH.d | 2 Hr |
| SA020314 | Inj07_SA24_BruinCSH.d | 3 Hr |
| SA020315 | Inj24_SA11_BruinCSH.d | 3 Hr |
| SA020316 | Inj18_SA23_BruinCSH.d | 3 Hr |
| SA020317 | Inj16_SA22_BruinCSH.d | 3 Hr |
| SA020318 | Inj12_SA10_BruinCSH.d | 3 Hr |
| SA020319 | Inj21_SA12_BruinCSH.d | 3 Hr |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO000428 |
| Collection Summary: | Liver biopsies were snap frozen in liquid nitrogen and stored at 80. Tissue was pulverized, while frozen and tissue was aliquoted into .6 ml tubes between 30 and 70 mg of liver tissue. 3 replicates are provided per sample. |
| Collection Protocol Filename: | StudyDesign_BoteBruinsma_072414.pdf |
| Sample Type: | Tissue |
| Storage Conditions: | -80 C |
| Tissue Cell Quantity Taken: | between 30 and 70 mg |
Treatment:
| Treatment ID: | TR000448 |
| Treatment Summary: | 2 livers (names 23 and 31) were perfused for 3 hours, providing 4 timecourse (0, 1, 2, 3) biopsies. 3 replicates for each biopsy (A, B ,C). These were the only 2 run on the Lipidomics platform. |
| Treatment Protocol Filename: | StudyDesign_BoteBruinsma_072414.pdf |
Sample Preparation:
| Sampleprep ID: | SP000441 |
| Sampleprep Summary: | 1. Weigh 4mg tissue sample in to a 2mL Eppendorf tube. 2. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. 3. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. 4. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500μL supernatant for analysis, and 500μL for a backup. Store backup aliquots in the -20°C freezer. 5. Evaporate one 500μl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). 6. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 7. Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. 8. Remove supernatant to a new Eppendorf tube. 9. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 10. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Liver_Tissue_Samples.pdf |
| Processing Method: | Homogenization |
Combined analysis:
| Analysis ID | AN000653 | AN000654 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6530 | Agilent 6550 |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | counts | counts |
Chromatography:
| Chromatography ID: | CH000471 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6530 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99%B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 V |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000472 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6550 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99%B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 5 uL |
| Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 V |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000579 |
| Analysis ID: | AN000653 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 V |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 L/min |
| Dry Gas Temp: | 325 C |
| Fragment Voltage: | 120 V |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 C |
| Ion Spray Voltage: | 1000 V |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 L/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 V |
| Resolution Setting: | extended dynamic range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 V |
| MS ID: | MS000580 |
| Analysis ID: | AN000654 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 V |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 13 L/min |
| Dry Gas Temp: | 200 C |
| Fragment Voltage: | 175 V |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 C |
| Ion Spray Voltage: | 1000 V |
| Ionization: | Neg |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 L/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 V |
| Resolution Setting: | extended dynamic range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 V |
