{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001747","ANALYSIS_ID":"AN002843","VERSION":"1","CREATED_ON":"April 20, 2021, 4:07 pm"},

"PROJECT":{"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"},

"STUDY":{"STUDY_TITLE":"Lung metabolomics after ischemic acute kidney injury reveals increased oxidative stress, altered energy production, and ATP depletion","STUDY_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_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"491",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"491"}
},
{
"Subject ID":"-",
"Sample ID":"493",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"493"}
},
{
"Subject ID":"-",
"Sample ID":"495",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"495"}
},
{
"Subject ID":"-",
"Sample ID":"497",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"497"}
},
{
"Subject ID":"-",
"Sample ID":"499",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"499"}
},
{
"Subject ID":"-",
"Sample ID":"502",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"502"}
},
{
"Subject ID":"-",
"Sample ID":"504",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"504"}
},
{
"Subject ID":"-",
"Sample ID":"508",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"508"}
},
{
"Subject ID":"-",
"Sample ID":"510",
"Factors":{"group":"sham","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"510"}
},
{
"Subject ID":"-",
"Sample ID":"496",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"496"}
},
{
"Subject ID":"-",
"Sample ID":"498",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"498"}
},
{
"Subject ID":"-",
"Sample ID":"500",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"500"}
},
{
"Subject ID":"-",
"Sample ID":"501",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"501"}
},
{
"Subject ID":"-",
"Sample ID":"503",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"503"}
},
{
"Subject ID":"-",
"Sample ID":"505",
"Factors":{"group":"AKI","time point":"7d"},
"Additional sample data":{"RAW_FILE_NAME":"505"}
},
{
"Subject ID":"-",
"Sample ID":"512",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"512"}
},
{
"Subject ID":"-",
"Sample ID":"514",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"514"}
},
{
"Subject ID":"-",
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"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"516"}
},
{
"Subject ID":"-",
"Sample ID":"518",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"518"}
},
{
"Subject ID":"-",
"Sample ID":"520",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"520"}
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{
"Subject ID":"-",
"Sample ID":"536",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"536"}
},
{
"Subject ID":"-",
"Sample ID":"538",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"538"}
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{
"Subject ID":"-",
"Sample ID":"540",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"540"}
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{
"Subject ID":"-",
"Sample ID":"542",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"542"}
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{
"Subject ID":"-",
"Sample ID":"544",
"Factors":{"group":"sham","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"544"}
},
{
"Subject ID":"-",
"Sample ID":"511",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"511"}
},
{
"Subject ID":"-",
"Sample ID":"513",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"513"}
},
{
"Subject ID":"-",
"Sample ID":"515",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"515"}
},
{
"Subject ID":"-",
"Sample ID":"517",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"517"}
},
{
"Subject ID":"-",
"Sample ID":"519",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"519"}
},
{
"Subject ID":"-",
"Sample ID":"537",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"537"}
},
{
"Subject ID":"-",
"Sample ID":"539",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"539"}
},
{
"Subject ID":"-",
"Sample ID":"541",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"541"}
},
{
"Subject ID":"-",
"Sample ID":"543",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"543"}
},
{
"Subject ID":"-",
"Sample ID":"545",
"Factors":{"group":"AKI","time point":"4h"},
"Additional sample data":{"RAW_FILE_NAME":"545"}
},
{
"Subject ID":"-",
"Sample ID":"521",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"521"}
},
{
"Subject ID":"-",
"Sample ID":"524",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"524"}
},
{
"Subject ID":"-",
"Sample ID":"527",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"527"}
},
{
"Subject ID":"-",
"Sample ID":"530",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"530"}
},
{
"Subject ID":"-",
"Sample ID":"533",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"533"}
},
{
"Subject ID":"-",
"Sample ID":"548",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"548"}
},
{
"Subject ID":"-",
"Sample ID":"551",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"551"}
},
{
"Subject ID":"-",
"Sample ID":"554",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"554"}
},
{
"Subject ID":"-",
"Sample ID":"557",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"557"}
},
{
"Subject ID":"-",
"Sample ID":"560",
"Factors":{"group":"sham","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"560"}
},
{
"Subject ID":"-",
"Sample ID":"522",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"522"}
},
{
"Subject ID":"-",
"Sample ID":"525",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"525"}
},
{
"Subject ID":"-",
"Sample ID":"528",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"528"}
},
{
"Subject ID":"-",
"Sample ID":"531",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"531"}
},
{
"Subject ID":"-",
"Sample ID":"534",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"534"}
},
{
"Subject ID":"-",
"Sample ID":"546",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"546"}
},
{
"Subject ID":"-",
"Sample ID":"549",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"549"}
},
{
"Subject ID":"-",
"Sample ID":"552",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"552"}
},
{
"Subject ID":"-",
"Sample ID":"555",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"555"}
},
{
"Subject ID":"-",
"Sample ID":"558",
"Factors":{"group":"AKI","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"558"}
},
{
"Subject ID":"-",
"Sample ID":"523",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"523"}
},
{
"Subject ID":"-",
"Sample ID":"526",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"526"}
},
{
"Subject ID":"-",
"Sample ID":"529",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"529"}
},
{
"Subject ID":"-",
"Sample ID":"532",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"532"}
},
{
"Subject ID":"-",
"Sample ID":"535",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"535"}
},
{
"Subject ID":"-",
"Sample ID":"547",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"547"}
},
{
"Subject ID":"-",
"Sample ID":"550",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"550"}
},
{
"Subject ID":"-",
"Sample ID":"553",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"553"}
},
{
"Subject ID":"-",
"Sample ID":"556",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"556"}
},
{
"Subject ID":"-",
"Sample ID":"559",
"Factors":{"group":"normal","time point":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"559"}
}
],
"COLLECTION":{"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_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."},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"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).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Phenomenex Kinetex C18 (150 x 2.1mm, 1.7 um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","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."},

"MS_METABOLITE_DATA":{
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