{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001949","ANALYSIS_ID":"AN003173","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Plasma Metabolome Normalization in Rheumatoid Arthritis following initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy","PROJECT_TYPE":"Clinical","PROJECT_SUMMARY":"Methotrexate (MTX) efficacy in the treatment of rheumatoid arthritis (RA) is variable and unpredictable, resulting in a need to identify biomarkers to guide drug therapy. This study evaluates changes in the plasma metabolome associated with response to MTX in RA with the goal of understanding the metabolic basis for MTX efficacy towards the identification of potential metabolic biomarkers of MTX response.","INSTITUTE":"University of Kansas","DEPARTMENT":"Pharmacy Practice","LABORATORY":"Funk","LAST_NAME":"Medcalf","FIRST_NAME":"Matthew","ADDRESS":"2106 Olathe Boulevard","EMAIL":"mmedcalf@ku.edu","PHONE":"13147880236","FUNDING_SOURCE":"KL2TR002367","DOI":"http://dx.doi.org/10.21228/M8Z10X"},

"STUDY":{"STUDY_TITLE":"Plasma Metabolome Normalization in Rheumatoid Arthritis following initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy","STUDY_TYPE":"Clinical","STUDY_SUMMARY":"Methotrexate (MTX) efficacy in the treatment of rheumatoid arthritis (RA) is variable and unpredictable, resulting in a need to identify biomarkers to guide drug therapy. This study evaluates changes in the plasma metabolome associated with response to MTX in RA with the goal of understanding the metabolic basis for MTX efficacy towards the identification of potential metabolic biomarkers of MTX response.","INSTITUTE":"University of Kansas","DEPARTMENT":"Pharmacy Practice","LABORATORY":"Funk","LAST_NAME":"Medcalf","FIRST_NAME":"Matthew","ADDRESS":"2106 Olathe Boulevard","EMAIL":"mmedcalf@ku.edu","PHONE":"13147880236","SUBMIT_DATE":"2021-10-20"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"21 - 84","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1_001",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"55","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"10_010",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"55","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"11_011",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Male","Age":"55","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"12_012",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"21","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"13_013",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"23","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"14_014",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"52","Race":"White","Smoke Status":"Former","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"15_015",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"57","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"16_016",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"60","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"17_017",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"58","Race":"Other","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"18_018",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"61","Race":"White","Smoke Status":"Former","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"19_019",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"44","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"2_002",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"54","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"20_020",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"69","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"3_003",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"44","Race":"Asian","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"4_004",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Male","Age":"41","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5_005",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"59","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"6_006",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"24","Race":"White","Smoke Status":"Current","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"7_007",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"53","Race":"White","Smoke Status":"Former","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"8_008",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Male","Age":"46","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"9_009",
"Factors":{"Condition":"Control"},
"Additional sample data":{"Sex":"Female","Age":"49","Race":"White","Smoke Status":"Never","MTX (mg/week)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"21_021",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"42","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"23_023",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"36","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"25_025",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"49","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"27_027",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"76","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"29_029",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"76","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"31_031",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"64","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"33_033",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"59","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"35_035",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"23","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"37_037",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"47","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"39_039",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"74","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"41_041",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"84","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"43_043",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"67","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"45_045",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"60","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"47_047",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"55","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"49_049",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"44","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"51_051",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"32","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"53_053",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"64","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"55_055",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"21","Race":"Hispanic","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"57_057",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Female","Age":"51","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"59_059",
"Factors":{"Condition":"RA"},
"Additional sample data":{"Sex":"Male","Age":"24","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"22_022",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"43","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"24_024",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"37","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"26_026",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"49","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"28_028",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"76","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"30_030",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"77","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"32_032",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"64","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"34_034",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"60","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"36_036",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"23","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"38_038",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"48","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"40_040",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"64","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"42_042",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"85","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"44_044",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"67","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"46_046",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"60","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"48_048",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"55","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"50_050",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"45","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"52_052",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"33","Race":"White","Smoke Status":"Current","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"54_054",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"65","Race":"White","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"56_056",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"21","Race":"Hispanic","Smoke Status":"Never","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"58_058",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Female","Age":"51","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
},
{
"Subject ID":"-",
"Sample ID":"60_060",
"Factors":{"Condition":"RA+MTX"},
"Additional sample data":{"Sex":"Male","Age":"24","Race":"White","Smoke Status":"Former","MTX (mg/week)":"15-20"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Venous blood samples were collected in 8.5 mL ACD Solution A BD Vacutainer tubes for the healthy control, and RA patients prior to initiation of MTX and at a 16 week follow up visit. Venous blood samples were collected and separated into plasma and cellular fractions by centrifugation at 3,000 RPM in a Thermo Scientific Sorvall Legend XTR centrifuge for 10 minutes. The resulting plasma supernatant was separated into aliquots and stored at -80 ⁰C prior to analysis.","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃","ADDITIVES":"ACD"},

"TREATMENT":{"TREATMENT_SUMMARY":"Biobanked plasma samples were acquired from a subset of RA patients (n=20) that participated in a 16-week multicenter open-label study that sought to evaluated predictors of MTX response in RA (ClinicalTrials.gov NCT03414502) (PMID: 32911284). The study included sites within the Rheumatology Arthritis Investigational Network (RAIN). For each patient, plasma samples at baseline and 16-weeks were provided for analysis. All patients received 15 mg/week of MTX and 1 mg/day of folic acid upon enrollment. The MTX does was escalated to 20 mg/week in patients that did not achieve clinical remission by 8 weeks, as tolerated.","TREATMENT_COMPOUND":"Methotrexate","TREATMENT_ROUTE":"Subcutaneous or Oral","TREATMENT_DOSE":"15-20 mg/week","TREATMENT_DOSEDURATION":"16 weeks"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma samples were sent to the West Coast Metabolomics Center and were processed according to laboratory Standard Operating Procedures for samples preparations of blood plasma or serum samples for lipidomic, biogenic amine, and primary metabolomic analysis using a biphasic MeOH/MTBE/Water extraction procedure. The upper organic phase was used for lipidomics analysis and the aqueous phase was used for analysis of primary metabolism and biogenic amines.","SAMPLEPREP_PROTOCOL_FILENAME":"Biogenic_Amines.Data Processing; Lipidomics.Data Processing; Primary_Metabolism.Data_Processing"},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Leco Pegasus IV","COLUMN_NAME":"Restek Rtx-5Sil (30m x 0.25mm,0.25um)","CHROMATOGRAPHY_TYPE":"GC"},

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

"MS":{"INSTRUMENT_NAME":"Leco Pegasus IV TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","MS_COMMENTS":"MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.","ION_MODE":"POSITIVE","MS_RESULTS_FILE":"ST001949_AN003173_Results.txt UNITS:Peak Height Intensity"},

"MS_METABOLITE_DATA":{
"Units":"Peak Height Intensity",

"Data":[{"Metabolite":"10-Hydroxydecanoic 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}