{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002696","ANALYSIS_ID":"AN004370","VERSION":"1","CREATED_ON":"08-16-2023"},

"PROJECT":{"PROJECT_TITLE":"Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice","PROJECT_TYPE":"MS Untargeted Lipidomics","PROJECT_SUMMARY":"Genetic association studies have linked ATP10A and closely related type IV P-type ATPases (P4-ATPases) to insulin resistance and vascular complications, such as atherosclerosis. In addition, prior studies of mice harboring large, overlapping chromosomal deletions implicated Atp10A in the development of diet-induced obesity and insulin resistance. Here, we generated gene-specific Atp10A knockout mice and show that Atp10A-/- mice fed a high-fat diet did not gain excess weight relative to wild-type littermates. However, Atp10A-/- mice displayed female-specific dyslipidemia characterized by elevated plasma triglycerides, free fatty acids and cholesterol, as well as altered VLDL and HDL properties. We also observed increased circulating levels of several sphingolipid species along with reduced levels of eicosanoids and bile acids. The Atp10A-/- mice also displayed hepatic insulin resistance without perturbations to whole-body glucose homeostasis. Thus, ATP10A has a sex-specific role in regulating plasma lipid composition and maintaining hepatic liver insulin sensitivity in mice.","INSTITUTE":"Vanderbilt University","DEPARTMENT":"Biological Sciences","LABORATORY":"Graham","LAST_NAME":"Graham","FIRST_NAME":"Todd","ADDRESS":"5260 Medical Research Building III BSB","EMAIL":"tr.graham@Vanderbilt.Edu","PHONE":"615-343-1835","PUBLICATIONS":"TBA","DOI":"http://dx.doi.org/10.21228/M83H7N"},

"STUDY":{"STUDY_TITLE":"Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice","STUDY_TYPE":"MS Untargeted Lipidomics","STUDY_SUMMARY":"Genetic association studies have linked ATP10A and closely related type IV P-type ATPases (P4-ATPases) to insulin resistance and vascular complications, such as atherosclerosis. In addition, prior studies of mice harboring large, overlapping chromosomal deletions implicated Atp10A in the development of diet-induced obesity and insulin resistance. Here, we generated gene-specific Atp10A knockout mice and show that Atp10A-/- mice fed a high-fat diet did not gain excess weight relative to wild-type littermates. However, Atp10A-/- mice displayed female-specific dyslipidemia characterized by elevated plasma triglycerides, free fatty acids and cholesterol, as well as altered VLDL and HDL properties. We also observed increased circulating levels of several sphingolipid species along with reduced levels of eicosanoids and bile acids. The Atp10A-/- mice also displayed hepatic insulin resistance without perturbations to whole-body glucose homeostasis. Thus, ATP10A has a sex-specific role in regulating plasma lipid composition and maintaining hepatic liver insulin sensitivity in mice.","INSTITUTE":"Vanderbilt University","DEPARTMENT":"Chemistry","LABORATORY":"Center for Innovative Technology","LAST_NAME":"May","FIRST_NAME":"Jody","ADDRESS":"2301 Vanderbilt Place, Nashville, TN, 37235, USA","EMAIL":"jody.c.may@vanderbilt.edu","PHONE":"615-875-8438","SUBMIT_DATE":"2023-04-20"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"Wild-type and ATP10A knockouts","AGE_OR_AGE_RANGE":"16-20 weeks","WEIGHT_OR_WEIGHT_RANGE":"23-28 grams","ANIMAL_HOUSING":"temperature and humidity-controlled facilities","ANIMAL_LIGHT_CYCLE":"12 h light/dark cycles","ANIMAL_FEED":"standard chow or 60% HFD (D12492, Research Diets) ad libitum,"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"KO1-1n",
"Sample ID":"ko1-1n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"46_KO1-1_neg.mzML"}
},
{
"Subject ID":"KO1-1p",
"Sample ID":"ko1-1p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"17_KO1-1_pos.mzML"}
},
{
"Subject ID":"KO1-2n",
"Sample ID":"ko1-2n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"58_KO1-2_neg.mzML"}
},
{
"Subject ID":"KO1-2p",
"Sample ID":"ko1-2p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"27_KO1-2_pos.mzML"}
},
{
"Subject ID":"KO2-1n",
"Sample ID":"ko2-1n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"48_KO2-1_neg.mzML"}
},
{
"Subject ID":"KO2-1p",
"Sample ID":"ko2-1p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"09_KO2-1_pos.mzML"}
},
{
"Subject ID":"KO2-2n",
"Sample ID":"ko2-2n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"57_KO2-2_neg.mzML"}
},
{
"Subject ID":"KO2-2p",
"Sample ID":"ko2-2p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"23_KO2-2_pos.mzML"}
},
{
"Subject ID":"KO3-1n",
"Sample ID":"ko3-1n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"50_KO3-1_neg.mzML"}
},
{
"Subject ID":"KO3-1p",
"Sample ID":"ko3-1p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"14_KO3-1_pos.mzML"}
},
{
"Subject ID":"KO3-2n",
"Sample ID":"ko3-2n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"63_KO3-2_neg.mzML"}
},
{
"Subject ID":"KO3-2p",
"Sample ID":"ko3-2p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"29_KO3-2_pos.mzML"}
},
{
"Subject ID":"KO4-1n",
"Sample ID":"ko4-1n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"52_KO4-1_neg.mzML"}
},
{
"Subject ID":"KO4-1p",
"Sample ID":"ko4-1p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"13_KO4-1_pos.mzML"}
},
{
"Subject ID":"KO4-2n",
"Sample ID":"ko4-2n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"55_KO4-2_neg.mzML"}
},
{
"Subject ID":"KO4-2p",
"Sample ID":"ko4-2p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"20_KO4-2_pos.mzML"}
},
{
"Subject ID":"KO5-1n",
"Sample ID":"ko5-1n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"45_KO5-1_neg.mzML"}
},
{
"Subject ID":"KO5-1p",
"Sample ID":"ko5-1p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"11_KO5-1_pos.mzML"}
},
{
"Subject ID":"KO5-2n",
"Sample ID":"ko5-2n",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"59_KO5-2_neg.mzML"}
},
{
"Subject ID":"KO5-2p",
"Sample ID":"ko5-2p",
"Factors":{"Genotype":"ATP10A-knockout"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"22_KO5-2_pos.mzML"}
},
{
"Subject ID":"WT1-1n",
"Sample ID":"wt1-1n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"49_WT1-1_neg.mzML"}
},
{
"Subject ID":"WT1-1p",
"Sample ID":"wt1-1p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"16_WT1-1_pos.mzML"}
},
{
"Subject ID":"WT1-2n",
"Sample ID":"wt1-2n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"62_WT1-2_neg.mzML"}
},
{
"Subject ID":"WT1-2p",
"Sample ID":"wt1-2p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"25_WT1-2_pos.mzML"}
},
{
"Subject ID":"WT2-1n",
"Sample ID":"wt2-1n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"51_WT2-1_neg.mzML"}
},
{
"Subject ID":"WT2-1p",
"Sample ID":"wt2-1p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"10_WT2-1_pos.mzML"}
},
{
"Subject ID":"WT2-2n",
"Sample ID":"wt2-2n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"61_WT2-2_neg.mzML"}
},
{
"Subject ID":"WT2-2p",
"Sample ID":"wt2-2p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"26_WT2-2_pos.mzML"}
},
{
"Subject ID":"WT3-1n",
"Sample ID":"wt3-1n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"44_WT3-1_neg.mzML"}
},
{
"Subject ID":"WT3-1p",
"Sample ID":"wt3-1p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"12_WT3-1_pos.mzML"}
},
{
"Subject ID":"WT3-2n",
"Sample ID":"wt3-2n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"64_WT3-2_neg.mzML"}
},
{
"Subject ID":"WT3-2p",
"Sample ID":"wt3-2p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"28_WT3-2_pos.mzML"}
},
{
"Subject ID":"WT4-1n",
"Sample ID":"wt4-1n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"47_WT4-1_neg.mzML"}
},
{
"Subject ID":"WT4-1p",
"Sample ID":"wt4-1p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"18_WT4-1_pos.mzML"}
},
{
"Subject ID":"WT4-2n",
"Sample ID":"wt4-2n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"60_WT4-2_neg.mzML"}
},
{
"Subject ID":"WT4-2p",
"Sample ID":"wt4-2p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"21_WT4-2_pos.mzML"}
},
{
"Subject ID":"WT5-1n",
"Sample ID":"wt5-1n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"3","RAW_FILE_NAME":"53_WT5-1_neg.mzML"}
},
{
"Subject ID":"WT5-1p",
"Sample ID":"wt5-1p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"1","RAW_FILE_NAME":"15_WT5-1_pos.mzML"}
},
{
"Subject ID":"WT5-2n",
"Sample ID":"wt5-2n",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"negative","Batch":"4","RAW_FILE_NAME":"56_WT5-2_neg.mzML"}
},
{
"Subject ID":"WT5-2p",
"Sample ID":"wt5-2p",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"Treatment":"OGTT","MS ion mode":"positive","Batch":"2","RAW_FILE_NAME":"24_WT5-2_pos.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Plasma was collected, via a retroorbital bleed or cardiac puncture, from 5-hr fasted mice and 5-hr fasted mice that had undergone an OGTT.","SAMPLE_TYPE":"Blood (plasma)","COLLECTION_METHOD":"retroorbital bleed or cardiac puncture","STORAGE_CONDITIONS":"-20℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mice were fasted for 5 hours (7AM-12PM). No additional treatments were administered.","TREATMENT":"WT vs KO","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":"5 hour","ANIMAL_ENDP_EUTHANASIA":"n/a","ANIMAL_ENDP_TISSUE_COLL_LIST":"Plasma was collected, via a retroorbital bleed or cardiac puncture","ANIMAL_ENDP_CLINICAL_SIGNS":"n/a"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"100 uL of plasma was collected from each mouse. An isotopically labeled lipid mixture (SPLASH LIPIDOMIX, Avanti) was added as an internal standard to each plasma sample. A liquid-liquid extraction was performed by adding 1 mL methyl tert-butyl ether (MTBE), vortexing, and subsequently centrifuging for 10 minutes at 10,000 rpm and 4˚C. The nonpolar, MTBE fraction (top liquid layer) containing the lipophilic components was removed and dried under vacuum centrifugation. Dried samples were stored at -80˚C until the day of MS analysis. For LC-IM-MS analysis, dried samples were resuspended in 100 µL IPA containing 40 µg/mL heptadecanoic acid and nonadecanoic acid, as well as 10 µg/mL glucosyl(β) sphingosine and N-heptadecanoyl-D-erythrosphingosine.","PROCESSING_STORAGE_CONDITIONS":"4℃","EXTRACTION_METHOD":"MTBE","EXTRACT_ENRICHMENT":"vacuum centrifuge","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"100 uL IPA","SAMPLE_DERIVATIZATION":"n/a","SAMPLE_SPIKING":"14 heavy-labeled lipids prior to extraction; 4 odd-chain lipids during reconstitution","SUBCELLULAR_LOCATION":"n/a"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"HPLC-IM-MS/MS on an Agilent 6560 mass spectrometer using a ZORBAX Extend-C18 RPLC column (Phase A: 0.1% formic acid and 10 mM NH4CHOO in water, Phase B: 0.1% formic acid and 10 mM NH4CHOO in 60:36:4 isopropanol:acetonitrile:water).","INSTRUMENT_NAME":"Agilent 6560","COLUMN_NAME":"Agilent ZORBAX RRHD Extend-C18 (50 x 2.1mm,1.8um)","COLUMN_TEMPERATURE":"40","FLOW_GRADIENT":"70% B for 1 min, 70-86% B in 2.5 min, 86% B for 6.5 min, 86-100% B in 1 min, 100% B for 6 min, 100-70% B in 0.1 min, and 70% B for 1.9 min.","FLOW_RATE":"300 ul/min","SOLVENT_A":"Water (10mM Amm. Formate) 0.1% formic acid","SOLVENT_B":"60:36:4 IPA:ACN:H2O (10mM Amm. Formate) 0.1% formic acid","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"LABORATORY_NAME":"Center for Innovative Technology","ANALYSIS_TYPE":"MS","ACQUISITION_DATE":"1/20/2021","SOFTWARE_VERSION":"MassHunter 10","OPERATOR_NAME":"Bailey S. Rose"},

"MS":{"INSTRUMENT_NAME":"Agilent 6560 Ion Mobility","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"Data alignment and biostatical analysis was performed using Progenesis QI (Waters).","ION_MODE":"NEGATIVE","MS_RESULTS_FILE":"ST002696_AN004370_Results.txt UNITS:Ion Abundances Has m/z:Yes Has RT:Yes RT units:Minutes"}

}