{
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"PROJECT":{"PROJECT_TITLE":"Predicting lupus membranous nephritis using reduced picolinic acid to tryptophan ratio as a urinary biomarker","PROJECT_TYPE":"MS quantitative analysis","PROJECT_SUMMARY":"The current gold standard for classifying lupus nephritis (LN) progression is a renal biopsy, which is an invasive procedure. Undergoing a series of biopsies for monitoring disease progression and treatments is unlikely suitable for patients with LN. Thus, there is an urgent need for non-invasive alternative biomarkers that can facilitate LN class diagnosis. Such biomarkers will be very useful in guiding intervention strategies to mitigate or treat patients with LN. Urine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Metabolomics was performed to identify potential metabolites, which could be specific for the classification of membranous LN. The ratio of picolinic acid (Pic) to tryptophan (Trp) ([Pic/Trp] ratio) was found to be a promising candidate for LN diagnostic and membranous classification. It has high potential as an alternative biomarker for the non-invasive diagnosis of LN.","INSTITUTE":"Mahidol University","DEPARTMENT":"Siriraj Metabolomics and Phenomics Center","LABORATORY":"Siriraj Center of Research Excellence in Metabolomics and Systems Biology","LAST_NAME":"Khoomrung","FIRST_NAME":"Sakda","ADDRESS":"2 Wanglang Road, Bangkok, Bangkok, 10700, Thailand","EMAIL":"sakda.kho@mahidol.edu","PHONE":"024195511","PUBLICATIONS":"https://doi.org/10.1016/j.isci.2021.103355"},

"STUDY":{"STUDY_TITLE":"Quantification of metabolites in kynurenine pathway","STUDY_SUMMARY":"Urine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Quantification of metabolites in kynurenine pathway was performed using LC-MS/MS.","INSTITUTE":"Mahidol University","DEPARTMENT":"Siriraj Metabolomics and Phenomics Center","LABORATORY":"Siriraj Center of Research Excellence in Metabolomics and Systems Biology","LAST_NAME":"Khoomrung","FIRST_NAME":"Sakda","ADDRESS":"2 Wanglang Road Bangkoknoi, Bangkok 10700, Thailand","EMAIL":"sakda.kho@mahidol.edu","PHONE":"024195511","NUM_GROUPS":"2","TOTAL_SUBJECTS":"117","PUBLICATIONS":"https://doi.org/10.1016/j.isci.2021.103355"},

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"Sample ID":"LN870",
"Factors":{"Sample_group":"LN","Disease_subclass":"All class V"},
"Additional sample data":{"RAW_FILE_NAME":"LN870.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN925",
"Factors":{"Sample_group":"LN","Disease_subclass":"All class V"},
"Additional sample data":{"RAW_FILE_NAME":"LN925.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Both morning urine and blood samples were collected under sterile conditions within the same day of biopsy/recruitment. Urine samples were centrifuged at 3,500 rpm for 10 min at 4°C. The supernatant was then aliquoted and stored at −80°C until the analysis. Common blood biochemical parameters were measured by an ISO 15189 accredited laboratory. Serum creatinine (SCr) and urine creatinine (UCr) were measured by an enzymatic assay using a Dimension ExL analyzer (Siemens Healthcare Diagnostics, Newark, DE, USA). Urine protein (Uprot) was measured by a modified pyrogallol red-molybdate method. Uprot was reported as urine protein creatinine ratio (UPCR in mg/mgCr). The estimated glomerular filtration rate (eGFR in mL/min/1.73 m2) was calculated using the CKD-EPI equation (Levey et al., 2009):","SAMPLE_TYPE":"Urine"},

"TREATMENT":{"TREATMENT_SUMMARY":"LN patients and health subjects (N) were recruited from Ramathibodi Hospital, Bangkok, Thailand. Patients, who fulfilled at least four of the American College of Rheumatology 1982 revised criteria for SLE (Hochberg, 1997) and were referred to kidney biopsy for clinical indications of proteinuria ≥ 0.5g/24 hours (Fanouriakis et al., 2020) were included."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The urine samples were prepared based on a previously published protocol (Zhu et al., 2019) with minor modifications. Briefly, a 50 μL of each urine sample was mixed with 200 μL of MeOH/ACN (1:1, v/v) containing 100 ng of anthranilic acid C13 (Ant-C13) as an internal standard (IS). The mixture was vortexed for 30 s and sonicated for 10 min (room temperature). The mixture was then left overnight (−20°C) for protein precipitation before centrifugation at 13,000 rpm (4°C) for 15 min. The supernatant was transferred to a new test tube and evaporated to dryness (room temperature) using a vacuum concentrator (Labconco, MO, USA). The dried sample was reconstituted in 100 μL of Milli-Q H2O (containing 0.1% formic acid), vortexed for 30 s, and sonicated (room temperature) for 10 min. The reconstituted sample was centrifuged at 13,000 rpm (4°C) for 15 min. The supernatant was kept at −80°C before analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"A volume of 5 μL of a standard or sample was injected onto an HSS T3 column, 2.1 × 100 mm, 1.8 μM column (Waters, Milford, MA, USA) at 30°C with a constant flow rate of 0.3 mL/min. Mobile phases consisted of (A) 0.1% formic acid in Milli-Q water and (B) 0.1% formic acid in ACN. The gradient program started at 99% A, decreased to 70% over 7.0 min, then decreased to 30% at 9 min, and return to the initial condition at 10 min and held for 4.0 min. The total runtime was 14 min. The weak and strong needles wash solutions were 5% ACN and H2O/ACN/MeOH/IPA (1:1:1:1), respectively.","CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic acid","FLOW_GRADIENT":"The gradient program started at 99% A, decreased to 70% over 7.0 min, then decreased to 30% at 9 min and return to the initial condition at 10 min and held for 4.0 min. The total runtime was 14 min. The weak and strong needles wash solutions were 5% ACN and H2O/ACN/MeOH/IPA (1:1:1:1), respectively.","FLOW_RATE":"0.4ml/min","COLUMN_TEMPERATURE":"30"},

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

"MS":{"INSTRUMENT_NAME":"Waters Xevo-TQ-S","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Quantitative analysis (absolute quantification) was achieved by external calibration curves of each standard prepared in pooled urine samples (standard addition) (Limjiasahapong et al., 2021). The linear ranges of the calibration standards are as follows: 3.5–1,000 ng/mL for Ant; 4.5–80 ng/mL for Cin; 8–2,500 ng/ml for Kyna; 8–5,000 ng/ml for Kyn; 1.4–400 ng/ml for Pic; 40–5000 ng/ml for Qui; 7–2000 ng/ml for Trp; 2–200 ng/ml for Xan; 900–14,000 ng/ml for 3OH-Kyn; 300–2,500 ng/ml for 3OH-Ant and 8–2,000 ng/ml for Ant-C13."},

"MS_METABOLITE_DATA":{
"Units":"ng/ml",

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"Metabolites":[{"metabolite_name":"Kynurenic acid"},{"metabolite_name":"Kynurenine"},{"metabolite_name":"Picolinic acid"},{"metabolite_name":"Quinolinic acid"},{"metabolite_name":"Trpptophan"},{"metabolite_name":"Xanthurenic acid"},{"metabolite_name":"3-OH-Kynurenine"},{"metabolite_name":"3-OH-Anthranilic acid"}]
}

}