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 |
Select appropriate tab below to view additional metadata details:
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 |
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. |
Combined analysis:
| Analysis ID | AN003026 | AN003027 | AN003028 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | GC | Unspecified | Unspecified |
| Chromatography system | Thermo-Finnigan Trace DSQ | Waters Acquity | Waters Acquity |
| Column | per Metabolon | per Metabolon | per Metabolon |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Single quadrupole | Single quadrupole | Single quadrupole |
| MS instrument name | Thermo LTQ-FT | Thermo LTQ-FT | Thermo LTQ-FT |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE |
| Units | Peak | Peak | Peak |
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: | Unspecified |
MS:
| MS ID: | MS002815 |
| Analysis ID: | AN003026 |
| Instrument Name: | Thermo LTQ-FT |
| Instrument Type: | Single quadrupole |
| MS Type: | ESI |
| MS Comments: | Bioinformatics: The informatics system consisted of four major components, the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these informatics components were the LAN backbone, and a database server running Oracle 10.2.0.1 Enterprise Edition. LIMS: The purpose of the Metabolon LIMS system was to enable fully auditable laboratory automation through a secure, easy to use, and highly specialized system. The scope of the Metabolon LIMS system encompasses sample accessioning, sample preparation and instrumental analysis and reporting and advanced data analysis. All of the subsequent software systems are grounded in the LIMS data structures. It has been modified to leverage and interface with the in-house information extraction and data visualization systems, as well as third party instrumentation and data analysis software. Data Extraction and Quality Assurance: The data extraction of the raw mass spec data files yielded information that could loaded into a relational database and manipulated without resorting to BLOB manipulation. Once in the database the information was examined and appropriate QC limits were imposed. Peaks were identified using Metabolon’s proprietary peak integration software, and component parts were stored in a separate and specifically designed complex data structure. Compound identification: Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Identification of known chemical entities was based on comparison to metabolomic library entries of purified standards. As of this writing, more than 1000 commercially available purified standard compounds had been acquired registered into LIMS for distribution to both the LC and GC platforms for determination of their analytical characteristics. The combination of chromatographic properties and mass spectra gave an indication of a match to the specific compound or an isobaric entity. Additional entities could be identified by virtue of their recurrent nature (both chromatographic and mass spectral). These compounds have the potential to be identified by future acquisition of a matching purified standard or by classical structural analysis. Curation: A variety of curation procedures were carried out to ensure that a high quality data set was made available for statistical analysis and data interpretation. The QC and curation processes were designed to ensure accurate and consistent identification of true chemical entities, and to remove those representing system artifacts, mis-assignments, and background noise. Metabolon data analysts use proprietary visualization and interpretation software to confirm the consistency of peak identification among the various samples. Library matches for each compound were checked for each sample and corrected if necessary. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002816 |
| Analysis ID: | AN003027 |
| Instrument Name: | Thermo LTQ-FT |
| Instrument Type: | Single quadrupole |
| MS Type: | ESI |
| MS Comments: | Accurate Mass Determination and MS/MS fragmentation (LC/MS), (LC/MS/MS): The LC/MS portion of the platform was based on a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ-FT mass spectrometer, which had a linear ion-trap (LIT) front end and a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer backend. For ions with counts greater than 2 million, an accurate mass measurement could be performed. Accurate mass measurements could be made on the parent ion as well as fragments. The typical mass error was less than 5 ppm. Ions with less than two million counts require a greater amount of effort to characterize. Fragmentation spectra (MS/MS) were typically generated in data dependent manner, but if necessary, targeted MS/MS could be employed, such as in the case of lower level signals. Bioinformatics: The informatics system consisted of four major components, the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these informatics components were the LAN backbone, and a database server running Oracle 10.2.0.1 Enterprise Edition. LIMS: The purpose of the Metabolon LIMS system was to enable fully auditable laboratory automation through a secure, easy to use, and highly specialized system. The scope of the Metabolon LIMS system encompasses sample accessioning, sample preparation and instrumental analysis and reporting and advanced data analysis. All of the subsequent software systems are grounded in the LIMS data structures. It has been modified to leverage and interface with the in-house information extraction and data visualization systems, as well as third party instrumentation and data analysis software. Data Extraction and Quality Assurance: The data extraction of the raw mass spec data files yielded information that could loaded into a relational database and manipulated without resorting to BLOB manipulation. Once in the database the information was examined and appropriate QC limits were imposed. Peaks were identified using Metabolon’s proprietary peak integration software, and component parts were stored in a separate and specifically designed complex data structure. Compound identification: Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Identification of known chemical entities was based on comparison to metabolomic library entries of purified standards. As of this writing, more than 1000 commercially available purified standard compounds had been acquired registered into LIMS for distribution to both the LC and GC platforms for determination of their analytical characteristics. The combination of chromatographic properties and mass spectra gave an indication of a match to the specific compound or an isobaric entity. Additional entities could be identified by virtue of their recurrent nature (both chromatographic and mass spectral). These compounds have the potential to be identified by future acquisition of a matching purified standard or by classical structural analysis. Curation: A variety of curation procedures were carried out to ensure that a high quality data set was made available for statistical analysis and data interpretation. The QC and curation processes were designed to ensure accurate and consistent identification of true chemical entities, and to remove those representing system artifacts, mis-assignments, and background noise. Metabolon data analysts use proprietary visualization and interpretation software to confirm the consistency of peak identification among the various samples. Library matches for each compound were checked for each sample and corrected if necessary. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002817 |
| Analysis ID: | AN003028 |
| Instrument Name: | Thermo LTQ-FT |
| Instrument Type: | Single quadrupole |
| MS Type: | ESI |
| MS Comments: | Accurate Mass Determination and MS/MS fragmentation (LC/MS), (LC/MS/MS): The LC/MS portion of the platform was based on a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ-FT mass spectrometer, which had a linear ion-trap (LIT) front end and a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer backend. For ions with counts greater than 2 million, an accurate mass measurement could be performed. Accurate mass measurements could be made on the parent ion as well as fragments. The typical mass error was less than 5 ppm. Ions with less than two million counts require a greater amount of effort to characterize. Fragmentation spectra (MS/MS) were typically generated in data dependent manner, but if necessary, targeted MS/MS could be employed, such as in the case of lower level signals. Bioinformatics: The informatics system consisted of four major components, the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these informatics components were the LAN backbone, and a database server running Oracle 10.2.0.1 Enterprise Edition. LIMS: The purpose of the Metabolon LIMS system was to enable fully auditable laboratory automation through a secure, easy to use, and highly specialized system. The scope of the Metabolon LIMS system encompasses sample accessioning, sample preparation and instrumental analysis and reporting and advanced data analysis. All of the subsequent software systems are grounded in the LIMS data structures. It has been modified to leverage and interface with the in-house information extraction and data visualization systems, as well as third party instrumentation and data analysis software. Data Extraction and Quality Assurance: The data extraction of the raw mass spec data files yielded information that could loaded into a relational database and manipulated without resorting to BLOB manipulation. Once in the database the information was examined and appropriate QC limits were imposed. Peaks were identified using Metabolon’s proprietary peak integration software, and component parts were stored in a separate and specifically designed complex data structure. Compound identification: Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Identification of known chemical entities was based on comparison to metabolomic library entries of purified standards. As of this writing, more than 1000 commercially available purified standard compounds had been acquired registered into LIMS for distribution to both the LC and GC platforms for determination of their analytical characteristics. The combination of chromatographic properties and mass spectra gave an indication of a match to the specific compound or an isobaric entity. Additional entities could be identified by virtue of their recurrent nature (both chromatographic and mass spectral). These compounds have the potential to be identified by future acquisition of a matching purified standard or by classical structural analysis. Curation: A variety of curation procedures were carried out to ensure that a high quality data set was made available for statistical analysis and data interpretation. The QC and curation processes were designed to ensure accurate and consistent identification of true chemical entities, and to remove those representing system artifacts, mis-assignments, and background noise. Metabolon data analysts use proprietary visualization and interpretation software to confirm the consistency of peak identification among the various samples. Library matches for each compound were checked for each sample and corrected if necessary. |
| Ion Mode: | NEGATIVE |
