Summary of Study ST001747

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 PR001119. The data can be accessed directly via it's Project DOI: 10.21228/M82D8P 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 IDST001747
Study TitleLung metabolomics after ischemic acute kidney injury reveals increased oxidative stress, altered energy production, and ATP depletion
Study SummaryAcute kidney injury (AKI) is a complex disease associated with increased mortality that may be due to deleterious distant organ effects. AKI associated with respiratory complications, in particular, has a poor outcome. In murine models, AKI is characterized by increased circulating cytokines, lung chemokine upregulation, and neutrophilic infiltration, similar to other causes of indirect acute lung injury (ALI)(e.g., sepsis). Many causes of lung inflammation are associated with a lung metabolic profile characterized by increased oxidative stress, a shift towards the use of other forms of energy production, and/or a depleted energy state. To our knowledge, there are no studies that have evaluated pulmonary energy production and metabolism after AKI. We hypothesized that based on the parallels between inflammatory acute lung injury and AKI-mediated lung injury, a similar metabolic profile would be observed. Lung metabolomics and ATP levels were assessed 4 hours, 24 hours, and 7 days after ischemic AKI in mice. Numerous novel findings regarding the effect of AKI on the lung were observed including 1) increased oxidative stress, 2) a shift toward alternate methods of energy production, and 3) depleted levels of ATP. The findings in this report bring to light novel characteristics of AKI-mediated lung injury and provide new leads into the mechanisms by which AKI in patients predisposes to pulmonary complications.
Institute
University of Colorado Anschutz Medical Campus
Last NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2021-04-15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-05-04
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M82D8P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001119
Project DOI:doi: 10.21228/M82D8P
Project Title:Lung metabolomics after ischemic acute kidney injury reveals increased oxidative stress, altered energy production, and ATP depletion
Project Summary:Acute kidney injury (AKI) is a complex disease associated with increased mortality that may be due to deleterious distant organ effects. AKI associated with respiratory complications, in particular, has a poor outcome. In murine models, AKI is characterized by increased circulating cytokines, lung chemokine upregulation, and neutrophilic infiltration, similar to other causes of indirect acute lung injury (ALI)(e.g., sepsis). Many causes of lung inflammation are associated with a lung metabolic profile characterized by increased oxidative stress, a shift towards the use of other forms of energy production, and/or a depleted energy state. To our knowledge, there are no studies that have evaluated pulmonary energy production and metabolism after AKI. We hypothesized that based on the parallels between inflammatory acute lung injury and AKI-mediated lung injury, a similar metabolic profile would be observed. Lung metabolomics and ATP levels were assessed 4 hours, 24 hours, and 7 days after ischemic AKI in mice. Numerous novel findings regarding the effect of AKI on the lung were observed including 1) increased oxidative stress, 2) a shift toward alternate methods of energy production, and 3) depleted levels of ATP. The findings in this report bring to light novel characteristics of AKI-mediated lung injury and provide new leads into the mechanisms by which AKI in patients predisposes to pulmonary complications.
Institute:University of Colorado Anschutz Medical Campus
Last Name:Haines
First Name:Julie
Address:12801 E 17th Ave, Room 1303
Email:julie.haines@cuanschutz.edu
Phone:3037243339

Subject:

Subject ID:SU001824
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 group time point
SA163433534AKI 24h
SA163434531AKI 24h
SA163435522AKI 24h
SA163436546AKI 24h
SA163437525AKI 24h
SA163438528AKI 24h
SA163439549AKI 24h
SA163440558AKI 24h
SA163441555AKI 24h
SA163442552AKI 24h
SA163443517AKI 4h
SA163444515AKI 4h
SA163445513AKI 4h
SA163446519AKI 4h
SA163447543AKI 4h
SA163448511AKI 4h
SA163449545AKI 4h
SA163450539AKI 4h
SA163451537AKI 4h
SA163452541AKI 4h
SA163453503AKI 7d
SA163454505AKI 7d
SA163455501AKI 7d
SA163456496AKI 7d
SA163457500AKI 7d
SA163458498AKI 7d
SA163459529normal 24h
SA163460523normal 24h
SA163461526normal 24h
SA163462556normal 24h
SA163463559normal 24h
SA163464553normal 24h
SA163465550normal 24h
SA163466532normal 24h
SA163467535normal 24h
SA163468547normal 24h
SA163469554sham 24h
SA163470560sham 24h
SA163471551sham 24h
SA163472557sham 24h
SA163473521sham 24h
SA163474548sham 24h
SA163475527sham 24h
SA163476524sham 24h
SA163477530sham 24h
SA163478533sham 24h
SA163479518sham 4h
SA163480520sham 4h
SA163481512sham 4h
SA163482536sham 4h
SA163483514sham 4h
SA163484540sham 4h
SA163485538sham 4h
SA163486544sham 4h
SA163487516sham 4h
SA163488542sham 4h
SA163489493sham 7d
SA163490497sham 7d
SA163491508sham 7d
SA163492510sham 7d
SA163493504sham 7d
SA163494502sham 7d
SA163495495sham 7d
SA163496499sham 7d
SA163497491sham 7d
Showing results 1 to 65 of 65

Collection:

Collection ID:CO001817
Collection Summary:Adult (8-10 week-old), male C57B/6 mice (Jackson Laboratories, Bar Harbor, ME), weighing between 20-25g were used. They were maintained on a standard diet and water was freely available. All experiments were conducted in adherence to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animal protocol was approved by the Animal Care and Use Committee of the University of Colorado, Denver. Surgical Protocol. To induce ischemic AKI (29), mice were anesthetized with intraperitoneal avertin (2,2,2-tribromoethanol; Sigma Aldrich, Milwaukee, WI), a laparotomy was performed, and both renal pedicles were clamped for 22 minutes. Mice received 500 µl saline with buprenex subcutaneous injection preceding surgery and 500 µl saline was administered by subcutaneous injection daily after surgery. The sham procedure is similar in all respects – including laparotomy - except that renal pedicle clamping is not performed. Collection and preparation of plasma and lung samples. Blood was obtained via cardiac puncture and centrifuged at 3000g at 4°C for ten minutes; plasma was collected and centrifuged a second time at 3000g for one minute. The lungs were collected, weighed, snap frozen in liquid nitrogen and stored at -80°C. In this experiment, lung, heart, kidney and liver were all rapidly collected and snap frozen for future metabolomics assessment (19); in order to limit time to freezing (and potential changes in metabolic phenotype due to death) no additional processing of tissue occurred and organs were not perfused prior to collection.
Sample Type:Lung

Treatment:

Treatment ID:TR001837
Treatment Summary:To induce ischemic AKI (29), mice were anesthetized with intraperitoneal avertin (2,2,2-tribromoethanol; Sigma Aldrich, Milwaukee, WI), a laparotomy was performed, and both renal pedicles were clamped for 22 minutes. Mice received 500 µl saline with buprenex subcutaneous injection preceding surgery and 500 µl saline was administered by subcutaneous injection daily after surgery. The sham procedure is similar in all respects – including laparotomy - except that renal pedicle clamping is not performed.

Sample Preparation:

Sampleprep ID:SP001830
Sampleprep Summary:Metabolomics analyses. Frozen lung tissue was milled with mortar and pestle in the presence of liquid nitrogen and weighed to the nearest 0.1 mg. At a tissue concentration of 40 mg/mL, the samples were extracted in ice-cold lysis/extraction buffer (5:3:2 MeOH:MeCN:water v/v/v) followed by agitation at 4°C for 30 minutes and centrifugation at 18,213 g for 10 minutes at 4°C. The supernatants (10 uL per injection) were immediately analyzed by UHPLC-MS.

Combined analysis:

Analysis ID AN002843 AN002844
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002104
Chromatography Summary:10 μl of tissue extracts were injected into a UHPLC system (Ultimate 3000, Thermo, San Jose, CA, USA) and separated through a 3 min isocratic elution on a Kinetex XB-C18 column (150 × 2.1 mm i.d., 1.7 μm particle size – Phenomenex, Torrance, CA, USA) at 250 μl/min (mobile phase: 5% acetonitrile, 95% 18 mΩ H2O, 0.1% formic acid; column temperature: 25°C).
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Column Temperature:25
Flow Gradient:isocratic
Flow Rate:251 ul/min
Solvent A:5% acetonitrile/95%water; 0.1% formic acid
Solvent B:isocratic
Chromatography Type:Reversed phase
  
Chromatography ID:CH002105
Chromatography Summary:10 μl of tissue extracts were injected into a UHPLC system (Ultimate 3000, Thermo, San Jose, CA, USA) and separated through a 3 min isocratic elution on a Kinetex XB-C18 column (150 × 2.1 mm i.d., 1.7 μm particle size – Phenomenex, Torrance, CA, USA) at 250 μl/min (mobile phase: 5% acetonitrile, 95% 18 mΩ H2O, 0.1% formic acid; column temperature: 25°C).
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Column Temperature:25
Flow Gradient:isocratic
Flow Rate:252 ul/min
Solvent A:5% acetonitrile/95%water; 0.1% formic acid
Solvent B:isocratic
Chromatography Type:Reversed phase

MS:

MS ID:MS002636
Analysis ID:AN002843
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The UHPLC system was coupled online with a QExactive mass spectrometer (Thermo, San Jose, CA, USA), scanning in Full MS mode (2 μscans) at 70,000 resolution from 60-900 m/z, with 4 kV spray voltage, 15 sheath gas and 5 auxiliary gas, operated in positive ion mode. Calibration was performed before each analysis using a positive calibration mix (Piercenet – Thermo Fisher, Rockford, IL, USA). Limits of detection (LOD) were characterized by determining the smallest injected amino acid amount required to provide a signal to noise (S/N) ratio greater than three using < 5 ppm error on the accurate intact mass. Based on a conservative definition for Limit of Quantitation (LOQ), these values were calculated to be three fold higher than determined LODs. MS data acquired from the QExactive was converted from .raw file format to.mzXML format using MassMatrix (Cleveland, OH, USA). Amino acid assignments were performed using MAVEN (Princeton, NJ, USA). The MAVEN software platform provides tools for peak picking, feature detection and metabolite assignment against the KEGG pathway database. Assignments were further confirmed using a process for chemical formula determination using isotopic patterns and accurate intact mass (Clasquin et al. 2012). Analyte retention times were confirmed by comparison with external standard retention times, as indicated above.
Ion Mode:NEGATIVE
  
MS ID:MS002637
Analysis ID:AN002844
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The UHPLC system was coupled online with a QExactive mass spectrometer (Thermo, San Jose, CA, USA), scanning in Full MS mode (2 μscans) at 70,000 resolution from 60-900 m/z, with 4 kV spray voltage, 15 sheath gas and 5 auxiliary gas, operated in positive ion mode. Calibration was performed before each analysis using a positive calibration mix (Piercenet – Thermo Fisher, Rockford, IL, USA). Limits of detection (LOD) were characterized by determining the smallest injected amino acid amount required to provide a signal to noise (S/N) ratio greater than three using < 5 ppm error on the accurate intact mass. Based on a conservative definition for Limit of Quantitation (LOQ), these values were calculated to be three fold higher than determined LODs. MS data acquired from the QExactive was converted from .raw file format to.mzXML format using MassMatrix (Cleveland, OH, USA). Amino acid assignments were performed using MAVEN (Princeton, NJ, USA). The MAVEN software platform provides tools for peak picking, feature detection and metabolite assignment against the KEGG pathway database. Assignments were further confirmed using a process for chemical formula determination using isotopic patterns and accurate intact mass (Clasquin et al. 2012). Analyte retention times were confirmed by comparison with external standard retention times, as indicated above.
Ion Mode:POSITIVE
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