Summary of Study ST001866
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 PR001178. The data can be accessed directly via it's Project DOI: 10.21228/M8F99F This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001866 |
| Study Title | Systemic metabolite changes due to PHD inhibition |
| Study Type | Comparative metabolomic analysis of serum metabolites detected by untargeted LC/MS and GC/MS platform |
| Study Summary | Prolonged cellular hypoxia leads to energetic failure and death. However, sublethal hypoxia can trigger an adaptive response called hypoxic preconditioning. While prolyl-hydroxylase (PHD) enzymes and hypoxia inducible factors (HIFs) have been identified as key elements of oxygen sensing machinery, the mechanisms by which hypoxic preconditioning protects against insults remain unclear. Here, we perform serum metabolomic profiling to assess alterations induced by hypoxic preconditioning. We discover that hypoxic preconditioning increases serum kynurenine levels and enhance kynurenine biotransformation leading to preservation of NAD+ in the post-ischemic kidney. Furthermore, we show that Indoleamine 2,3-dioxygenase 1 (Ido1) deficiency abolishes the systemic increase of kynurenine and the subsequent renoprotection generated by hypoxic preconditioning. Importantly, exogenous administration of kynurenine restores the hypoxic preconditioning in the context of Ido1 deficiency. Collectively, our findings demonstrate a critical role of Ido1/kynurenine axis in mediating hypoxic preconditioning |
| Institute | Northwestern University |
| Department | Medicine/Nephrology |
| Laboratory | Kapitsinou |
| Last Name | Kapitsinou |
| First Name | Pinelopi |
| Address | 303 East Superior Street |
| pinelopi.kapitsinou@northwestern.edu | |
| Phone | 312-503-8710 |
| Submit Date | 2021-07-03 |
| Num Groups | 2 |
| Total Subjects | 14 |
| Num Males | 14 |
| Study Comments | N/A |
| Publications | Accepted in Cell Reports |
| Chear Study | No |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-01-02 |
| Release Version | 1 |
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Project:
| Project ID: | PR001178 |
| Project DOI: | doi: 10.21228/M8F99F |
| Project Title: | Systemic metabolic responses to hypoxia |
| Project Summary: | Prolonged cellular hypoxia leads to energetic failure and death. However, sublethal hypoxia can trigger an adaptive response called hypoxic preconditioning. While prolyl-hydroxylase (PHD) enzymes and hypoxia inducible factors (HIFs) have been identified as key elements of oxygen sensing machinery, the mechanisms by which hypoxic preconditioning protects against insults remain unclear. Here, we perform serum metabolomic profiling to assess alterations induced by hypoxic preconditioning. |
| Institute: | Northwestern University, Feinberg School of Medicine |
| Last Name: | Kapitsinou |
| First Name: | Pinelopi |
| Address: | 303 East Superior Street, Chicago, Il, 60611, USA |
| Email: | pinelopi.kapitsinou@northwestern.edu |
| Phone: | 312-503-8710 |
Subject:
| Subject ID: | SU001943 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA174494 | PHI_7 | PHI |
| SA174495 | PHI_1 | PHI |
| SA174496 | PHI_5 | PHI |
| SA174497 | PHI_6 | PHI |
| SA174498 | PHI_2 | PHI |
| SA174499 | PHI_3 | PHI |
| SA174500 | PHI_4 | PHI |
| SA174501 | Veh_11 | Vehicle |
| SA174502 | Veh_12 | Vehicle |
| SA174503 | Veh_10 | Vehicle |
| SA174504 | Veh_6 | Vehicle |
| SA174505 | Veh_7 | Vehicle |
| SA174506 | Veh_8 | Vehicle |
| SA174507 | Veh_9 | Vehicle |
| Showing results 1 to 14 of 14 |
Collection:
| Collection ID: | CO001936 |
| Collection Summary: | Whole blood was collected in BD Microtainer Serum Separator Tubes. After collection of the whole blood, blood was allowed to clot by leaving it undisturbed at room temperature for 20 minutes. Clot was removed by centrifuging at 1,000–2,000 x g for 10 minutes in a refrigerated centrifuge. The resulting supernatant(serum) was transferred into clean polypropylene tubes and stored at –80°C until time of analysis. |
| Sample Type: | Blood (serum) |
Treatment:
| Treatment ID: | TR001955 |
| Treatment Summary: | Serum was collected form mice subjected to pharmacologic PHD inhibition or treatment with vehicle. Specifically, mice were treated with two doses of PHD inhibitor ( IOX2, 60 mg/kg by gavage, 48hrs and 6 hrs prior to collection time) while control mice received vehicle. |
Sample Preparation:
| Sampleprep ID: | SP001949 |
| Sampleprep Summary: | The metabolomic screening was conducted by Metabolon, Inc (Durham, NC). The sample preparation process was carried out using the automated MicroLab STAR® system from Hamilton Company. Sample preparation was conducted using a proprietary series of organic and aqueous extractions to remove the protein fraction while allowing maximum recovery of small molecules. The resulting extract was divided into two fractions; one for analysis by LC and one for analysis by GC. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. Each sample was then frozen and dried under vacuum. Samples were then prepared for the appropriate instrument, either LC/MS or GC/MS. |
Chromatography:
| Chromatography ID: | CH002242 |
| Chromatography Summary: | The samples destined for GC/MS analysis were re-dried under vacuum desiccation for a minimum of 24 hours prior to being derivatized under dried nitrogen using bistrimethyl-silyl-triflouroacetamide (BSTFA). The GC column was 5% phenyl and the temperature ramp is from 40° to 300° C in a 16 minute period. Samples were analyzed on a Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer using electron impact ionization. The instrument was tuned and calibrated for mass resolution and mass accuracy on a daily basis. |
| Instrument Name: | Thermo-Finnigan Trace DSQ |
| Column Name: | per Metabolon |
| Chromatography Type: | GC |
| Chromatography ID: | CH002243 |
| Chromatography Summary: | The LC/MS portion of the platform was based on a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ mass spectrometer, which consisted of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer. The sample extract was split into two aliquots, dried, then reconstituted in acidic or basic LC-compatible solvents, each of which contained 11 or more injection standards at fixed concentrations. One aliquot was analyzed using acidic positive ion optimized conditions and the other using basic negative ion optimized conditions in two independent injections using separate dedicated columns. Extracts reconstituted in acidic conditions were gradient eluted using water and methanol both containing 0.1% Formic acid, while the basic extracts, which also used water/methanol, contained 6.5mM Ammonium Bicarbonate. |
| Instrument Name: | Waters Acquity |
| Column Name: | per Metabolon |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN003026 |
| Analysis Type: | MS |
| Chromatography ID: | CH002242 |
| Num Factors: | 2 |
| Num Metabolites: | 119 |
| Units: | Peak |
| Analysis ID: | AN003027 |
| Analysis Type: | MS |
| Chromatography ID: | CH002243 |
| Num Factors: | 2 |
| Num Metabolites: | 124 |
| Rt Units: | Seconds |
| Units: | Peak |
| Analysis ID: | AN003028 |
| Analysis Type: | MS |
| Chromatography ID: | CH002243 |
| Num Factors: | 2 |
| Num Metabolites: | 126 |
| Rt Units: | Seconds |
| Units: | Peak |
