Summary of Study ST000412
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 | ST000412 |
| Study Title | Metabolic profiling during ex vivo machine perfusion of the human liver (part I) |
| 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 | 2016-06-30 |
| Publications | doi:10.1038/srep22415 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | peg |
| Analysis Type Detail | GC-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: | SU000433 |
| 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 | Treatment | Collection Time |
|---|---|---|---|
| SA020200 | 140404ajlsa44_1 | fresh liver | 1 Hr |
| SA020201 | 140404ajlsa17_1 | fresh liver | 1 Hr |
| SA020202 | 140403ajlsa12_1 | fresh liver | 1 Hr |
| SA020203 | 140404ajlsa15_1 | fresh liver | 2 Hr |
| SA020204 | 140404ajlsa28_1 | fresh liver | 2 Hr |
| SA020205 | 140403ajlsa19_1 | fresh liver | 2 Hr |
| SA020206 | 140403ajlsa30_1 | fresh liver | 3 Hr |
| SA020207 | 140404ajlsa21_1 | fresh liver | 3 Hr |
| SA020208 | 140403ajlsa02_1 | fresh liver | 3 Hr |
| SA020209 | 140404ajlsa02_1 | nonwarm ischemic liver | - |
| SA020210 | 140404ajlsa06_1 | nonwarm ischemic liver | - |
| SA020211 | 140404ajlsa04_1 | nonwarm ischemic liver | - |
| SA020212 | 140403ajlsa34_1 | nonwarm ischemic liver | - |
| SA020213 | 140403ajlsa13_1 | nonwarm ischemic liver | - |
| SA020214 | 140404ajlsa07_1 | nonwarm ischemic liver | - |
| SA020215 | 140403ajlsa15_1 | nonwarm ischemic liver | 1 Hr |
| SA020216 | 140404ajlsa37_1 | nonwarm ischemic liver | 1 Hr |
| SA020217 | 140404ajlsa22_1 | nonwarm ischemic liver | 1 Hr |
| SA020218 | 140404ajlsa01_1 | nonwarm ischemic liver | 1 Hr |
| SA020219 | 140404ajlsa42_1 | nonwarm ischemic liver | 1 Hr |
| SA020220 | 140403ajlsa40_1 | nonwarm ischemic liver | 1 Hr |
| SA020221 | 140403ajlsa37_1 | nonwarm ischemic liver | 2 Hr |
| SA020222 | 140404ajlsa16_1 | nonwarm ischemic liver | 2 Hr |
| SA020223 | 140404ajlsa27_1 | nonwarm ischemic liver | 2 Hr |
| SA020224 | 140404ajlsa36_1 | nonwarm ischemic liver | 2 Hr |
| SA020225 | 140404ajlsa35_1 | nonwarm ischemic liver | 2 Hr |
| SA020226 | 140403ajlsa41_1 | nonwarm ischemic liver | 2 Hr |
| SA020227 | 140403ajlsa03_1 | nonwarm ischemic liver | 3 Hr |
| SA020228 | 140404ajlsa25_1 | nonwarm ischemic liver | 3 Hr |
| SA020229 | 140404ajlsa40_1 | nonwarm ischemic liver | 3 Hr |
| SA020230 | 140404ajlsa34_1 | nonwarm ischemic liver | 3 Hr |
| SA020231 | 140512actsa18_1 | nonwarm ischemic liver | 3 Hr |
| SA020232 | 140512actsa07_1 | nonwarm ischemic liver | 3 Hr |
| SA020233 | 140512actsa17_1 | nonwarm ischemic liver | 3 Hr |
| SA020234 | 140403ajlsa09_1 | nonwarm ischemic liver | 3 Hr |
| SA020235 | 140404ajlsa03_1 | nonwarm ischemic liver | 3 Hr |
| SA020236 | 140404ajlsa10_1 | steatotic liver | - |
| SA020237 | 140403ajlsa33_1 | steatotic liver | - |
| SA020238 | 140403ajlsa27_1 | steatotic liver | - |
| SA020239 | 140404ajlsa19_1 | steatotic liver | - |
| SA020240 | 140403ajlsa44_1 | steatotic liver | - |
| SA020241 | 140404ajlsa26_1 | steatotic liver | - |
| SA020242 | 140404ajlsa23_1 | steatotic liver | 1 Hr |
| SA020243 | 140403ajlsa01_1 | steatotic liver | 1 Hr |
| SA020244 | 140404ajlsa33_1 | steatotic liver | 1 Hr |
| SA020245 | 140404ajlsa14_1 | steatotic liver | 2 Hr |
| SA020246 | 140403ajlsa16_1 | steatotic liver | 2 Hr |
| SA020247 | 140403ajlsa31_1 | steatotic liver | 2 Hr |
| SA020248 | 140403ajlsa08_1 | steatotic liver | 3 Hr |
| SA020249 | 140404ajlsa20_1 | steatotic liver | 3 Hr |
| SA020250 | 140403ajlsa50_1 | steatotic liver | 3 Hr |
| SA020251 | 140404ajlsa12_1 | warm ischemic liver | - |
| SA020252 | 140404ajlsa32_1 | warm ischemic liver | - |
| SA020253 | 140404ajlsa09_1 | warm ischemic liver | - |
| SA020254 | 140512actsa03_1 | warm ischemic liver | - |
| SA020255 | 140404ajlsa41_1 | warm ischemic liver | - |
| SA020256 | 140403ajlsa11_1 | warm ischemic liver | - |
| SA020257 | 140404ajlsa45_1 | warm ischemic liver | - |
| SA020258 | 140512actsa19_1 | warm ischemic liver | - |
| SA020259 | 140512actsa01_1 | warm ischemic liver | - |
| SA020260 | 140403ajlsa47_1 | warm ischemic liver | - |
| SA020261 | 140404ajlsa05_1 | warm ischemic liver | - |
| SA020262 | 140403ajlsa35_1 | warm ischemic liver | - |
| SA020263 | 140403ajlsa45_1 | warm ischemic liver | 1 Hr |
| SA020264 | 140512actsa13_1 | warm ischemic liver | 1 Hr |
| SA020265 | 140512actsa06_1 | warm ischemic liver | 1 Hr |
| SA020266 | 140403ajlsa05_1 | warm ischemic liver | 1 Hr |
| SA020267 | 140404ajlsa39_1 | warm ischemic liver | 1 Hr |
| SA020268 | 140403ajlsa49_1 | warm ischemic liver | 1 Hr |
| SA020269 | 140403ajlsa25_1 | warm ischemic liver | 1 Hr |
| SA020270 | 140512actsa16_1 | warm ischemic liver | 1 Hr |
| SA020271 | 140403ajlsa36_1 | warm ischemic liver | 1 Hr |
| SA020272 | 140403ajlsa04_1 | warm ischemic liver | 1 Hr |
| SA020273 | 140403ajlsa17_1 | warm ischemic liver | 1 Hr |
| SA020274 | 140403ajlsa14_1 | warm ischemic liver | 1 Hr |
| SA020275 | 140403ajlsa21_1 | warm ischemic liver | 2 Hr |
| SA020276 | 140404ajlsa11_1 | warm ischemic liver | 2 Hr |
| SA020277 | 140403ajlsa22_1 | warm ischemic liver | 2 Hr |
| SA020278 | 140404ajlsa29_1 | warm ischemic liver | 2 Hr |
| SA020279 | 140403ajlsa20_1 | warm ischemic liver | 2 Hr |
| SA020280 | 140512actsa15_1 | warm ischemic liver | 2 Hr |
| SA020281 | 140512actsa11_1 | warm ischemic liver | 2 Hr |
| SA020282 | 140404ajlsa43_1 | warm ischemic liver | 2 Hr |
| SA020283 | 140404ajlsa24_1 | warm ischemic liver | 2 Hr |
| SA020284 | 140404ajlsa08_1 | warm ischemic liver | 2 Hr |
| SA020285 | 140512actsa05_1 | warm ischemic liver | 2 Hr |
| SA020286 | 140404ajlsa30_1 | warm ischemic liver | 2 Hr |
| SA020287 | 140512actsa09_1 | warm ischemic liver | 3 Hr |
| SA020288 | 140512actsa20_1 | warm ischemic liver | 3 Hr |
| SA020289 | 140512actsa02_1 | warm ischemic liver | 3 Hr |
| SA020290 | 140403ajlsa18_1 | warm ischemic liver | 3 Hr |
| SA020291 | 140403ajlsa42_1 | warm ischemic liver | 3 Hr |
| SA020292 | 140403ajlsa26_1 | warm ischemic liver | 3 Hr |
| SA020293 | 140403ajlsa06_1 | warm ischemic liver | 3 Hr |
| SA020294 | 140404ajlsa13_1 | warm ischemic liver | 3 Hr |
| SA020295 | 140403ajlsa24_1 | warm ischemic liver | 3 Hr |
| Showing results 1 to 96 of 96 |
Collection:
| Collection ID: | CO000427 |
| Collection Summary: | Liver biopsies were frozen in liquid nitrogen and then stored at -80. They were then pulverized and the crushed tissue from one biopsy was divided into three 0.6mL tubes, containing ±25-70mg. These are triplicates from each biopsy. Tissue was kept at cryo temperatures throughout. |
| Collection Protocol Filename: | StudyDesign_BoteBruinsma_02.11.14.pdf |
| Sample Type: | Tissue |
Treatment:
| Treatment ID: | TR000447 |
| Treatment Summary: | 9 livers were run for metabolites at 4 timepoints (0,1,2,3), in triplicate. Warm ischemic livers (27, 8, 34) and non-warm ischemic livers (25, 28, 35) and fresh liver samples (R). Liver 30 was a steatotic liver, for which there were 4 timepoints. |
| Treatment Protocol Filename: | StudyDesign_BoteBruinsma_02.11.14.pdf |
Sample Preparation:
| Sampleprep ID: | SP000440 |
| Sampleprep Summary: | 1. Weigh 4 mg tissue sample ( muscle 20 mg) in to a 2.0 ml eppendorf tube. Add 1.0 mL extraction solvent to the tissue sample and using GenoGrinder homogenize samples for 45 seconds ensuring that sample resembles a powder. 2. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 3. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 4. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) (only for liver and brain samples). 5. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 6. Remove supernatant to a new Eppendorff tube. 7. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 8. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Liver_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000652 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus III GC |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000470 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Leco Pegasus III GC |
| Column Name: | Restek Corporation Rtx-5Sil MS |
| Column Pressure: | 7.7 PSI |
| Column Temperature: | 50-330C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50 C ramped to 250 C by 12 C/s |
| Sample Injection: | 0.5 uL |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000578 |
| Analysis ID: | AN000652 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250 C |
| Ionization Energy: | 70 eV |
| Mass Accuracy: | Nominal |
| Source Temperature: | 250 C |
| Scan Range Moverz: | 85-500 Da |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 85-500 Da |
| Skimmer Voltage: | 1850 V |
