{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003335","ANALYSIS_ID":"AN005465","PROJECT_ID":"PR002074","VERSION":"1","CREATED_ON":"July 20, 2024, 7:15 am"}, "PROJECT":{"PROJECT_TITLE":"Biological stress metabolomics in Duchenne muscular dystrophy rodent model","PROJECT_TYPE":"Biological Stress Discovery Targeted Metabolomics","PROJECT_SUMMARY":"Our goal is to identify stress-relevant metabolomic alterations in dystrophin-deficient organisms following physiological stress exposure. Here we performed a targeted mass spectrometry-based plasma metabolomics screen through Metabolon that focused on biological stress pathways in healthy and dystrophin-deficient mdx mice exposed to mild scruff stress. One-third of the stress-relevant metabolites interrogated displayed significant elevation or depletion in mdx plasma after scruff stress and were restored to WT by skeletal muscle-specific dystrophin expression. The metabolic pathways of mdx mice altered by scruff stress are associated with regulation of the hypothalamic-pituitary-adrenal axis, locomotor tone, neurocognitive function, redox metabolism, cellular bioenergetics, and protein catabolism. Our data suggest that a mild stress triggers an exaggerated, multi-system metabolic response in mdx mice.","INSTITUTE":"University of Minnesota","DEPARTMENT":"Biochemistry, Molecular Biology, and Biophysics","LABORATORY":"James Ervasti","LAST_NAME":"Johnson","FIRST_NAME":"Erynn","ADDRESS":"420 Washington Ave SE","EMAIL":"joh18358@umn.edu","PHONE":"4024054007","FUNDING_SOURCE":"5T32AR007612-21; 5T32AR007612-22; 5T32AG029796-13; 5T32AG029796-14; 5R01AR042423-27; 5R01AR049899-18","CONTRIBUTORS":"Erynn E. Johnson; James M. Ervasti"}, "STUDY":{"STUDY_TITLE":"Biological stress metabolomics in Duchenne muscular dystrophy rodent model","STUDY_TYPE":"Biological Stress Discovery Targeted Metabolomics","STUDY_SUMMARY":"Duchenne muscular dystrophy is a severe neuromuscular wasting disease that is caused by a primary defect in dystrophin protein and involves organism-wide comorbidities such as cardiomyopathy, metabolic and mitochondrial dysfunction, and non-progressive cognitive impairments. Physiological stress exposure in the mdx mouse model of Duchenne muscular dystrophy results in phenotypic abnormalities that include locomotor inactivity, hypotension, and increased morbidity. Severe and lethal stress susceptibility in mdx mice corresponds to metabolic dysfunction in several coordinated metabolic pathways within dystrophin-deficient skeletal muscle, as well as prolonged elevation in mdx plasma corticosterone levels that extends beyond the WT stress response. Here we performed a targeted mass spectrometry-based plasma metabolomics screen focused on biological stress pathways in healthy and dystrophin-deficient mdx mice exposed to mild scruff stress. One-third of the stress-relevant metabolites interrogated displayed significant elevation or depletion in mdx plasma after scruff stress and were restored to WT by skeletal muscle-specific dystrophin expression. The metabolic pathways of mdx mice altered by scruff stress are associated with regulation of the hypothalamic-pituitary-adrenal axis, locomotor tone, neurocognitive function, redox metabolism, cellular bioenergetics, and protein catabolism. Our data suggest that a mild stress triggers an exaggerated, multi-system metabolic response in mdx mice.","INSTITUTE":"University of Minnesota","DEPARTMENT":"Biochemistry, Molecular Biology, and Biophysics","LABORATORY":"James Ervasti","LAST_NAME":"Johnson","FIRST_NAME":"Erynn","ADDRESS":"420 Washington Ave SE","EMAIL":"joh18358@umn.edu","PHONE":"4024054007","NUM_GROUPS":"6","TOTAL_SUBJECTS":"48","NUM_MALES":"48"}, "SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL6/J; C57BL10/J; C57BL/10ScSn-Dmdmdx/J","AGE_OR_AGE_RANGE":"120-150 days","WEIGHT_OR_WEIGHT_RANGE":"25-35g","HEIGHT_OR_HEIGHT_RANGE":"N/A","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratories","ANIMAL_HOUSING":"Research Animal Resources campus facilities","ANIMAL_LIGHT_CYCLE":"12h light/dark cycle","ANIMAL_FEED":"Standard chow","ANIMAL_WATER":"Water bottle","ANIMAL_INCLUSION_CRITERIA":"Age; gender"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"UNMN-01552", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01553", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01554", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01555", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01556", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01557", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01558", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01559", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01560", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01561", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01562", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01563", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01564", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01565", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01566", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01567", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01568", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01569", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01570", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01571", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01572", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01573", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01574", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01575", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01576", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01577", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01578", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01579", "Factors":{"GENOTYPE":"WT","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01580", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01581", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01582", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01583", "Factors":{"GENOTYPE":"MDX","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01584", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01585", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01586", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01587", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"no stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01588", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01589", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01590", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01591", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01592", "Factors":{"GENOTYPE":"WT","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01593", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01594", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01595", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01596", "Factors":{"GENOTYPE":"MDX","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01597", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01598", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} }, { "Subject ID":"-", "Sample ID":"UNMN-01599", "Factors":{"GENOTYPE":"MTBD","TREATMENT":"stress","Sample source":"mouse plasma"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Blood was collected after euthanasia via cardiac puncture and plasma was extracted and stored at -80 degrees Celsius until sample submission to Metabolon.","SAMPLE_TYPE":"Blood (plasma)","COLLECTION_METHOD":"Blood was collected after euthanasia via cardiac puncture and was rotated end-over-end in EDTA-coated tubes for 15 minutes at room temperature. Samples were centrifuged for 10 minutes at 2,000xg at 4 degrees Celsius, then plasma supernatant was collected and stored at -80 degrees Celsius until sample submission to Metabolon.","COLLECTION_LOCATION":"-80 degree freezer","COLLECTION_FREQUENCY":"Single collection","COLLECTION_DURATION":"30 minutes","VOLUMEORAMOUNT_COLLECTED":"200 microliters","STORAGE_CONDITIONS":"-80℃","COLLECTION_VIALS":"EDTA-coated centrifuge tubes","STORAGE_VIALS":"Centrifuge tubes","COLLECTION_TUBE_TEMP":"20-25 degrees Celsius","ADDITIVES":"EDTA"}, "TREATMENT":{"TREATMENT_SUMMARY":"Mice in the no stress group were euthanized and blood samples were collected following euthanasia. Mice in the stress group were monitored in open-field activity cages to measure total locomotion distance for 30 minutes, then were briefly handled by a standard scruff method for 30 seconds, followed by an additional 30 minute activity cage monitoring session and euthanasia/sample collection.","TREATMENT":"Scruff handling stress","TREATMENT_COMPOUND":"N/A","TREATMENT_ROUTE":"N/A","TREATMENT_DOSE":"N/A","TREATMENT_DOSEVOLUME":"N/A","TREATMENT_DOSEDURATION":"N/A","TREATMENT_VEHICLE":"N/A","ANIMAL_VET_TREATMENTS":"N/A","ANIMAL_ANESTHESIA":"N/A","ANIMAL_ACCLIMATION_DURATION":"N/A","ANIMAL_FASTING":"N/A","ANIMAL_ENDP_EUTHANASIA":"Tribromoethanol (Avertin)","ANIMAL_ENDP_TISSUE_COLL_LIST":"Blood","ANIMAL_ENDP_CLINICAL_SIGNS":"N/A"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma samples were pipetted in 200 microliter quantities into barcoded sample tubes and submitted to Metabolon for additional sample preparation and analysis. Sample preparation details are proprietary information held by Metabolon.","PROCESSING_METHOD":"N/A","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"N/A","EXTRACT_ENRICHMENT":"N/A","EXTRACT_CLEANUP":"N/A","SAMPLE_RESUSPENSION":"N/A","SAMPLE_DERIVATIZATION":"N/A","SAMPLE_SPIKING":"N/A","SUBCELLULAR_LOCATION":"N/A"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Low pH Lipophilic (LC/MS Pos late)","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2mm, 1.7um)","SOLVENT_A":"100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5","SOLVENT_B":"50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5","FLOW_GRADIENT":"Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.","FLOW_RATE":"0.60 mL/min","COLUMN_TEMPERATURE":"40-50"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"Other","ION_MODE":"POSITIVE","MS_COMMENTS":"Metabolon (LC/MS Pos late)"}, "MS_METABOLITE_DATA":{ "Units":"Peak Area", "Data":[{"Metabolite":"biliverdin","UNMN-01552":"1082979","UNMN-01553":"1801860","UNMN-01554":"2980326","UNMN-01555":"522223","UNMN-01556":"5363076","UNMN-01557":"4819547","UNMN-01558":"","UNMN-01559":"6766001","UNMN-01560":"4056095","UNMN-01561":"5763942","UNMN-01562":"4322014","UNMN-01563":"2688469","UNMN-01564":"1035425","UNMN-01565":"3372515","UNMN-01566":"4033795","UNMN-01567":"1092693","UNMN-01568":"2535855","UNMN-01569":"11254082","UNMN-01570":"9214698","UNMN-01571":"8381081","UNMN-01572":"3045479","UNMN-01573":"6507383","UNMN-01574":"1963635","UNMN-01575":"5894282","UNMN-01576":"2236951","UNMN-01577":"1660435","UNMN-01578":"2739179","UNMN-01579":"3199444","UNMN-01580":"10889134","UNMN-01581":"4869696","UNMN-01582":"7290637","UNMN-01583":"10346302","UNMN-01584":"4633343","UNMN-01585":"5231599","UNMN-01586":"","UNMN-01587":"6756579","UNMN-01588":"691898","UNMN-01589":"2213937","UNMN-01590":"1094219","UNMN-01591":"","UNMN-01592":"4022458","UNMN-01593":"6082190","UNMN-01594":"12045030","UNMN-01595":"2612226","UNMN-01596":"7682206","UNMN-01597":"7518083","UNMN-01598":"832844","UNMN-01599":"1832889"},{"Metabolite":"sphingosine","UNMN-01552":"7298678","UNMN-01553":"9394172","UNMN-01554":"5370124","UNMN-01555":"5283545","UNMN-01556":"9710956","UNMN-01557":"11715808","UNMN-01558":"8052925","UNMN-01559":"5806694","UNMN-01560":"5638397","UNMN-01561":"4953104","UNMN-01562":"5606514","UNMN-01563":"7207631","UNMN-01564":"10033528","UNMN-01565":"4119672","UNMN-01566":"7804894","UNMN-01567":"5315287","UNMN-01568":"3483174","UNMN-01569":"7332114","UNMN-01570":"5041820","UNMN-01571":"5256584","UNMN-01572":"4520178","UNMN-01573":"10642194","UNMN-01574":"2890772","UNMN-01575":"7496113","UNMN-01576":"4742048","UNMN-01577":"8105332","UNMN-01578":"8958347","UNMN-01579":"8113540","UNMN-01580":"9060858","UNMN-01581":"7366497","UNMN-01582":"10977870","UNMN-01583":"4484231","UNMN-01584":"7121822","UNMN-01585":"6752873","UNMN-01586":"10728693","UNMN-01587":"4123254","UNMN-01588":"7739644","UNMN-01589":"5574806","UNMN-01590":"11956106","UNMN-01591":"4557000","UNMN-01592":"8175040","UNMN-01593":"7078320","UNMN-01594":"5287663","UNMN-01595":"6002472","UNMN-01596":"6282576","UNMN-01597":"5723532","UNMN-01598":"5680786","UNMN-01599":"5463033"},{"Metabolite":"sphinganine","UNMN-01552":"2754669","UNMN-01553":"3818028","UNMN-01554":"2515706","UNMN-01555":"2084224","UNMN-01556":"1889896","UNMN-01557":"2536248","UNMN-01558":"2604926","UNMN-01559":"1611320","UNMN-01560":"1995040","UNMN-01561":"2269942","UNMN-01562":"2205420","UNMN-01563":"2919829","UNMN-01564":"3629189","UNMN-01565":"1585884","UNMN-01566":"3374214","UNMN-01567":"2092798","UNMN-01568":"1428643","UNMN-01569":"2568242","UNMN-01570":"2148803","UNMN-01571":"1930329","UNMN-01572":"1942856","UNMN-01573":"4935329","UNMN-01574":"1605390","UNMN-01575":"2964708","UNMN-01576":"1511002","UNMN-01577":"2920014","UNMN-01578":"2827102","UNMN-01579":"3280890","UNMN-01580":"2618295","UNMN-01581":"1594816","UNMN-01582":"3425026","UNMN-01583":"2259290","UNMN-01584":"2508814","UNMN-01585":"2342067","UNMN-01586":"4927243","UNMN-01587":"1613875","UNMN-01588":"4752005","UNMN-01589":"2371133","UNMN-01590":"5506523","UNMN-01591":"2578499","UNMN-01592":"3687438","UNMN-01593":"2978638","UNMN-01594":"2229433","UNMN-01595":"1727520","UNMN-01596":"2598675","UNMN-01597":"2216894","UNMN-01598":"2131348","UNMN-01599":"2288975"},{"Metabolite":"retinol 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