{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002214","ANALYSIS_ID":"AN003622","VERSION":"1","CREATED_ON":"July 12, 2022, 10:40 am"},

"PROJECT":{"PROJECT_TITLE":"The effects of PKM2 modulation and hypoxia on the metabolic landscape of Alzheimer patient-derived induced neurons","PROJECT_SUMMARY":"We have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed.","INSTITUTE":"University of Colorado Denver","LABORATORY":"Lab of Angelo D'Alessandro in collaboration with lab of Jerome Mertens (Univ of Innsbruck)","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"STUDY":{"STUDY_TITLE":"The effects of PKM2 modulation and hypoxia on the metabolic landscape of Alzheimer patient-derived induced neurons","STUDY_SUMMARY":"We have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed.","INSTITUTE":"University of Colorado Denver","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"50-90 yrs"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"3131-C",
"Factors":{"Condition":"Alzheimer patient","Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-1"}
},
{
"Subject ID":"-",
"Sample ID":"3131-S",
"Factors":{"Condition":"Alzheimer patient","Treatment":"Shikonin"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-3"}
},
{
"Subject ID":"-",
"Sample ID":"3053-C",
"Factors":{"Condition":"Alzheimer patient","Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-5"}
},
{
"Subject ID":"-",
"Sample ID":"3053-S",
"Factors":{"Condition":"Alzheimer patient","Treatment":"Shikonin"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-7"}
},
{
"Subject ID":"-",
"Sample ID":"8020-C",
"Factors":{"Condition":"Alzheimer patient","Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-9"}
},
{
"Subject ID":"-",
"Sample ID":"8020-S",
"Factors":{"Condition":"Alzheimer patient","Treatment":"Shikonin"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-11"}
},
{
"Subject ID":"-",
"Sample ID":"2800-C",
"Factors":{"Condition":"Alzheimer patient","Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-13"}
},
{
"Subject ID":"-",
"Sample ID":"2800-S",
"Factors":{"Condition":"Alzheimer patient","Treatment":"Shikonin"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-15"}
},
{
"Subject ID":"-",
"Sample ID":"2608-C",
"Factors":{"Condition":"non-demented control","Treatment":"GFP-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-17"}
},
{
"Subject ID":"-",
"Sample ID":"2608-OE",
"Factors":{"Condition":"non-demented control","Treatment":"PKM2-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-18"}
},
{
"Subject ID":"-",
"Sample ID":"8011-C",
"Factors":{"Condition":"non-demented control","Treatment":"GFP-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-19"}
},
{
"Subject ID":"-",
"Sample ID":"8011-OE",
"Factors":{"Condition":"non-demented control","Treatment":"PKM2-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-20"}
},
{
"Subject ID":"-",
"Sample ID":"8011-DFO",
"Factors":{"Condition":"non-demented control","Treatment":"CoDo Treatment"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-21"}
},
{
"Subject ID":"-",
"Sample ID":"2785-C",
"Factors":{"Condition":"non-demented control","Treatment":"GFP-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-22"}
},
{
"Subject ID":"-",
"Sample ID":"2785-OE",
"Factors":{"Condition":"non-demented control","Treatment":"PKM2-overexpression"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-23"}
},
{
"Subject ID":"-",
"Sample ID":"2785-DFO",
"Factors":{"Condition":"non-demented control","Treatment":"CoDo Treatment"},
"Additional sample data":{"RAW_FILE_NAME":"MR36-24"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"For Metabolome, iNs were flow cytometry-isolated 21 days of conversion. iNs were sorted based on the expression of the PSA-NCAM surface markers using PSA-NCAM-PE (Miltenyi) and re-plated on Geltrex-coated wells. The following day, iNs were treated with 2.5 mM DGlucose-C13 for 6 hours and harvested using Tryple. Supernatant and cell pellets were shock frozen in liquid nitrogen.","SAMPLE_TYPE":"Biopsy"},

"TREATMENT":{"TREATMENT_SUMMARY":"After two weeks of conversion, cells were treated for 10 days with shikonin (10 µM, ChemCruz) before FACS sorting. Control iNs were FACS-sorted and plated on Geltrex-coated wells before transduction with pLVXTP-EGFP-PKM2 or pLVXTP-EGFP. Around 60 % of all neurons were successfully transduced. Five days after transduction, iNs were harvested for MS-analysis. Alternatively, cells were treated with CoDo for 6 hours before harvest."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites from frozen cell pellets were extracted at 150,000 cells/mL in cold 5:3:2 MeOH:acetonitrile:water. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C). Supernatants were split into two equal tubes and gently dried using a vacuum concentrator. One set of residues were resuspended in 12 uL of 0.1% formic acid (for positive ion mode). The other set of residues were resuspended in 12 uL of 1 mM ammonium acetate (for negative ion mode)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Negative C18 cells","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Phenomenex Kinetex C18 2.1 x 150 mm, 1.7 um","SAMPLE_INJECTION":"10 uL"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database."},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"dAMP","3131-C":"8698.363","3053-C":"7426.417","8020-C":"8423.361","2800-C":"7044.199","2608-C":"9537.36","8011-C":"8682.341","2785-C":"7659.17","3131-S":"17786.48","3053-S":"16565.23","8020-S":"9340.69","2800-S":"5567.291","2608-OE":"10290.04","8011-OE":"20328.4","2785-OE":"12761.64","8011-DFO":"4939.935","2785-DFO":"8523.719"},{"Metabolite":"dCMP","3131-C":"18106.84","3053-C":"12643.76","8020-C":"18691.69","2800-C":"13855.19","2608-C":"18535.58","8011-C":"19082.22","2785-C":"17449.67","3131-S":"28185.16","3053-S":"26349.17","8020-S":"22559.44","2800-S":"9480.604","2608-OE":"16186.61","8011-OE":"36955.8","2785-OE":"36406.25","8011-DFO":"6288.346","2785-DFO":"0"},{"Metabolite":"2',3'-Cyclic CMP","3131-C":"15536.93","3053-C":"12155.62","8020-C":"18338.95","2800-C":"7597.142","2608-C":"15392","8011-C":"24252.85","2785-C":"14159.78","3131-S":"26469.65","3053-S":"25856.12","8020-S":"23985.45","2800-S":"12885.97","2608-OE":"9775.735","8011-OE":"38799.95","2785-OE":"43326.52","8011-DFO":"3296.335","2785-DFO":"0"},{"Metabolite":"UDP-glucose","3131-C":"9225.375","3053-C":"4387.281","8020-C":"14858.42","2800-C":"5246.401","2608-C":"10953.94","8011-C":"9931.653","2785-C":"4131.906","3131-S":"18422.71","3053-S":"10495.27","8020-S":"11047.78","2800-S":"8744.188","2608-OE":"10123.17","8011-OE":"21301.77","2785-OE":"13193.1","8011-DFO":"0","2785-DFO":"0"},{"Metabolite":"Phosphate","3131-C":"63421910","3053-C":"50400140","8020-C":"74532060","2800-C":"91823960","2608-C":"94394330","8011-C":"49109160","2785-C":"68457760","3131-S":"66822090","3053-S":"57828630","8020-S":"98450790","2800-S":"52413810","2608-OE":"146029400","8011-OE":"88570180","2785-OE":"83214020","8011-DFO":"199778400","2785-DFO":"193063000"},{"Metabolite":"Diphosphate","3131-C":"7107586","3053-C":"5027406","8020-C":"9217669","2800-C":"9813512","2608-C":"12212620","8011-C":"5307097","2785-C":"7544398","3131-S":"7003068","3053-S":"5972100","8020-S":"11565840","2800-S":"6021240","2608-OE":"19258740","8011-OE":"9363520","2785-OE":"10060660","8011-DFO":"26835490","2785-DFO":"25344520"},{"Metabolite":"D-Glucose","3131-C":"362824.8","3053-C":"483750.1","8020-C":"353864.9","2800-C":"288063.7","2608-C":"245480.1","8011-C":"420020.3","2785-C":"367578.4","3131-S":"480316.8","3053-S":"510257.4","8020-S":"390168.8","2800-S":"305124.4","2608-OE":"299636.6","8011-OE":"754697.2","2785-OE":"390516.4","8011-DFO":"93525.4","2785-DFO":"62192.28"},{"Metabolite":"D-Glyceraldehyde 3-phosphate/Glycerone phosphate","3131-C":"156736.9","3053-C":"62239.52","8020-C":"192731.8","2800-C":"77514.23","2608-C":"129983.7","8011-C":"80303.42","2785-C":"89817.5","3131-S":"137813.1","3053-S":"152200.2","8020-S":"40691.15","2800-S":"128698.7","2608-OE":"174803.4","8011-OE":"614163.4","2785-OE":"49632.51","8011-DFO":"6558.595","2785-DFO":"4170.484"},{"Metabolite":"2/3-Phospho-D-glycerate","3131-C":"156736.9","3053-C":"62239.52","8020-C":"192731.8","2800-C":"77514.23","2608-C":"129983.7","8011-C":"80303.42","2785-C":"89817.5","3131-S":"137813.1","3053-S":"152200.2","8020-S":"128698.7","2800-S":"40691.15","2608-OE":"174803.4","8011-OE":"614163.4","2785-OE":"49632.51","8011-DFO":"6558.595","2785-DFO":"4170.484"},{"Metabolite":"Phosphoenolpyruvate","3131-C":"25019.55","3053-C":"12221.58","8020-C":"23240.05","2800-C":"18224.95","2608-C":"23803.34","8011-C":"13100.15","2785-C":"9300.866","3131-S":"25474.38","3053-S":"30062.85","8020-S":"6585.779","2800-S":"8797.708","2608-OE":"34063.74","8011-OE":"127171.5","2785-OE":"5064.1","8011-DFO":"2067.09","2785-DFO":"0"},{"Metabolite":"Lactate","3131-C":"1538848","3053-C":"2782565","8020-C":"2332704","2800-C":"6177034","2608-C":"1919105","8011-C":"7293848","2785-C":"2385349","3131-S":"2961188","3053-S":"4349398","8020-S":"1957746","2800-S":"3672666","2608-OE":"1845232","8011-OE":"1886110","2785-OE":"2527975","8011-DFO":"981915.1","2785-DFO":"1546692"},{"Metabolite":"Maltose","3131-C":"8907.681","3053-C":"36746.84","8020-C":"32818.59","2800-C":"53051.46","2608-C":"46331.81","8011-C":"31827.07","2785-C":"50712.95","3131-S":"312253","3053-S":"39016.46","8020-S":"46981.57","2800-S":"10031.48","2608-OE":"34361.03","8011-OE":"9674.745","2785-OE":"23153.16","8011-DFO":"18553.48","2785-DFO":"34158.29"},{"Metabolite":"Maltotriose","3131-C":"14739.79","3053-C":"17038.73","8020-C":"16602.95","2800-C":"74746.49","2608-C":"13389.44","8011-C":"10652.63","2785-C":"15625.31","3131-S":"17800.7","3053-S":"11304.02","8020-S":"11018.87","2800-S":"13554.23","2608-OE":"14290.98","8011-OE":"15460.59","2785-OE":"11214.57","8011-DFO":"13524.79","2785-DFO":"18232.32"},{"Metabolite":"Mannitol","3131-C":"63967.51","3053-C":"146251.4","8020-C":"45167.46","2800-C":"156700","2608-C":"37267.49","8011-C":"128331.9","2785-C":"45524.84","3131-S":"105580.2","3053-S":"166284.8","8020-S":"58045.91","2800-S":"29092.58","2608-OE":"40337.45","8011-OE":"98778.48","2785-OE":"81625.46","8011-DFO":"30020.98","2785-DFO":"78348.6"},{"Metabolite":"Citrate","3131-C":"491482.3","3053-C":"623103.8","8020-C":"861660.3","2800-C":"2793952","2608-C":"1330968","8011-C":"1027024","2785-C":"921850.6","3131-S":"900203.4","3053-S":"1213030","8020-S":"1083270","2800-S":"491126","2608-OE":"1004159","8011-OE":"1104433","2785-OE":"1071646","8011-DFO":"874627","2785-DFO":"914965.7"},{"Metabolite":"2-Oxoglutaramate","3131-C":"10160.83","3053-C":"15135.68","8020-C":"9182.937","2800-C":"22655.79","2608-C":"24100.81","8011-C":"11942.21","2785-C":"13286.21","3131-S":"26958.18","3053-S":"20294.9","8020-S":"13291.42","2800-S":"13262.75","2608-OE":"10315.8","8011-OE":"16016.4","2785-OE":"25197","8011-DFO":"59782.79","2785-DFO":"19539.13"},{"Metabolite":"Succinate","3131-C":"242844.2","3053-C":"432249.6","8020-C":"198636.7","2800-C":"567978.2","2608-C":"299422.7","8011-C":"278764","2785-C":"170777.7","3131-S":"364957.2","3053-S":"335984.6","8020-S":"241483.2","2800-S":"189284.1","2608-OE":"228697.2","8011-OE":"327206.7","2785-OE":"344245.4","8011-DFO":"247010.5","2785-DFO":"360944.3"},{"Metabolite":"Fumarate","3131-C":"16756.59","3053-C":"41482.12","8020-C":"23797.42","2800-C":"41503.58","2608-C":"32056.89","8011-C":"22280.22","2785-C":"16754.75","3131-S":"21464.97","3053-S":"60352.2","8020-S":"34980.46","2800-S":"26742.44","2608-OE":"28178.72","8011-OE":"27808.57","2785-OE":"27122.15","8011-DFO":"7027.039","2785-DFO":"14166.9"},{"Metabolite":"Malate","3131-C":"328949.8","3053-C":"499910.1","8020-C":"644982.4","2800-C":"964666.7","2608-C":"669392.2","8011-C":"391439.4","2785-C":"362706","3131-S":"583184.3","3053-S":"517380.4","8020-S":"672316.3","2800-S":"331348.8","2608-OE":"589609.4","8011-OE":"645829.5","2785-OE":"453728.1","8011-DFO":"267034.9","2785-DFO":"472282.4"},{"Metabolite":"Oxaloacetate","3131-C":"62740.75","3053-C":"45201.44","8020-C":"36387.04","2800-C":"48787.06","2608-C":"39116.63","8011-C":"35646.02","2785-C":"46600.53","3131-S":"49050.53","3053-S":"35933.69","8020-S":"42086.34","2800-S":"32584.35","2608-OE":"48240.18","8011-OE":"45890.05","2785-OE":"38515","8011-DFO":"57477.17","2785-DFO":"59357.68"},{"Metabolite":"Sedoheptulose 1-phosphate","3131-C":"34684.73","3053-C":"9958.817","8020-C":"35681.03","2800-C":"31807.46","2608-C":"168357.6","8011-C":"24243.72","2785-C":"12627.79","3131-S":"35356.29","3053-S":"79948.9","8020-S":"4103.978","2800-S":"4510.142","2608-OE":"9242.829","8011-OE":"295663","2785-OE":"8033.564","8011-DFO":"0","2785-DFO":"0"},{"Metabolite":"alpha-D-Ribose 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