{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002269","ANALYSIS_ID":"AN003709","VERSION":"1","CREATED_ON":"02-08-2024"}, "PROJECT":{"PROJECT_TITLE":"Targeted plasma metabolomics in pediatric NAFLD patients","PROJECT_SUMMARY":"Several adult omics studies have been conducted to understand the pathophysiology of nonalcoholic fatty liver disease (NAFLD). However, the histological features of children are different from those of adults, and the onset and progression of pediatric NAFLD are not fully understood. In this study, we aimed to evaluate the metabolome profile and metabolic pathway changes associated with pediatric NAFLD to elucidate its pathophysiology. We analyzed the metabolic profiles of healthy control, lean NAFLD, overweight control and overweight NAFLD groups of children and adolescent participants (n = 165) by assessing plasma samples, and identified 18 NAFLD-specific metabolic features and metabolic changes in lipid, glutathione-related amino acid, and branched-chain amino acid metabolism by comparing control and NAFLD group in pediatric population with overweight. Metabolome changes in the plasma of pediatric patients with NAFLD are associated with the pathophysiology of the disease and can be utilized as a less-invasive approach to diagnose the disease.","INSTITUTE":"Seoul National University College of Medicine and Hospital","DEPARTMENT":"Department of Clinical Pharmacology and Therapeutics","LAST_NAME":"Chae","FIRST_NAME":"Woori","ADDRESS":"101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea","EMAIL":"yunus@snu.ac.kr","PHONE":"82-2-740-8905","FUNDING_SOURCE":"National Research Foundation (NRF) grant funded by the Korea government (Ministry of Science and ICT) [grant number NRF-2019R1F1A1057588]","DOI":"http://dx.doi.org/10.21228/M85H8N"}, "STUDY":{"STUDY_TITLE":"Targeted plasma metabolomics in pediatric NAFLD patients","STUDY_SUMMARY":"Several adult omics studies have been conducted to understand the pathophysiology of nonalcoholic fatty liver disease (NAFLD). However, the histological features of children are different from those of adults, and the onset and progression of pediatric NAFLD are not fully understood. In this study, we aimed to evaluate the metabolome profile and metabolic pathway changes associated with pediatric NAFLD to elucidate its pathophysiology. We analyzed the metabolic profiles of healthy control, lean NAFLD, overweight control and overweight NAFLD groups of children and adolescent participants (n = 165) by assessing plasma samples, and identified 18 NAFLD-specific metabolic features and metabolic changes in lipid, glutathione-related amino acid, and branched-chain amino acid metabolism by comparing control and NAFLD group in pediatric population with overweight. Metabolome changes in the plasma of pediatric patients with NAFLD are associated with the pathophysiology of the disease and can be utilized as a less-invasive approach to diagnose the disease.","INSTITUTE":"Seoul National University College of Medicine and Hospital","DEPARTMENT":"Department of Clinical Pharmacology and Therapeutics","LAST_NAME":"Chae","FIRST_NAME":"Woori","ADDRESS":"101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea","EMAIL":"yunus@snu.ac.kr","PHONE":"82-2-740-8905","SUBMIT_DATE":"2022-08-07"}, "SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"8.7-18.6 (year)","GENDER":"Male and female","HUMAN_ETHNICITY":"Korean","HUMAN_INCLUSION_CRITERIA":"We recruited children and adolescent participants who visited the pediatric departments of the Hallym University Sacred Heart Hospital and Seoul National University Children’s Hospital from January 2019 to May 2020, after obtaining informed consent from the children and their parents.","HUMAN_EXCLUSION_CRITERIA":"We excluded participants who were taking alcohol or medications known to affect the results of liver function tests. Participants with viral hepatitis, such as hepatitis A, B, or C, or with Epstein–Barr virus, Wilson’s disease, autoimmune hepatitis, or muscular disease were also excluded."}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"H_C_203", "Factors":{"Group":"Healthy Control"}, "Additional sample data":{"Age (year)":"15.9","Sex":"Male","BMI z-score":"-0.84","RAW_FILE_NAME":"KIT2-0-1211_1036510688_19_0_1_1_00_1036509184.raw","RAW_FILE_NAME":"KIT2-0-1212_1036510692_19_0_1_1_00_1036509184.raw","RAW_FILE_NAME":"KIT3-0-1211_1036510703_19_0_1_1_00_1036509184.raw","RAW_FILE_NAME":"KIT3-0-1212_1036510718_19_0_1_1_00_1036509184.raw"} }, { "Subject ID":"-", "Sample ID":"H_C_204", "Factors":{"Group":"Healthy Control"}, "Additional sample data":{"Age (year)":"16.4","Sex":"Female","BMI 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z-score":"-","RAW_FILE_NAME":"KIT2-0-1211_1036510722_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT2-0-1212_1036510737_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1211_1036510741_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1212_1036510756_84_0_1_1_00_1036503021.raw"} }, { "Subject ID":"-", "Sample ID":"Plasma_QC_6", "Factors":{"Group":"QC"}, "Additional sample data":{"Age (year)":"-","Sex":"-","BMI z-score":"-","RAW_FILE_NAME":"KIT2-0-1211_1036510722_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT2-0-1212_1036510737_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1211_1036510741_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1212_1036510756_96_0_1_1_00_1036503021.raw"} }, { "Subject ID":"-", "Sample ID":"Plasma_QC_7", "Factors":{"Group":"QC"}, "Additional sample data":{"Age (year)":"-","Sex":"-","BMI z-score":"-","RAW_FILE_NAME":"KIT2-0-1211_1036511280_72_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT2-0-1212_1036511294_72_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1211_1036511305_72_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1212_1036511310_72_0_1_1_00_1036503021.raw"} }, { "Subject ID":"-", "Sample ID":"Plasma_QC_8", "Factors":{"Group":"QC"}, "Additional sample data":{"Age (year)":"-","Sex":"-","BMI z-score":"-","RAW_FILE_NAME":"KIT2-0-1211_1036511280_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT2-0-1212_1036511294_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1211_1036511305_84_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1212_1036511310_84_0_1_1_00_1036503021.raw"} }, { "Subject ID":"-", "Sample ID":"Plasma_QC_9", "Factors":{"Group":"QC"}, "Additional sample data":{"Age (year)":"-","Sex":"-","BMI z-score":"-","RAW_FILE_NAME":"KIT2-0-1211_1036511280_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT2-0-1212_1036511294_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1211_1036511305_96_0_1_1_00_1036503021.raw","RAW_FILE_NAME":"KIT3-0-1212_1036511310_96_0_1_1_00_1036503021.raw"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"For metabolomic analysis, 4 mL of blood was collected from each participant after overnight fasting and centrifuged at 4℃. Separated plasma samples were collected and stored until use at -80℃.","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃"}, "TREATMENT":{"TREATMENT_SUMMARY":"We recruited children and adolescent participants who visited the pediatric departments of the Hallym University Sacred Heart Hospital and Seoul National University Children’s Hospital from January 2019 to May 2020, and evaluated the presence and grade of fatty liver by ultrasonography. The grade of steatosis was evaluated as follows by comparing hepatic echogenicity to kidney parenchyma: normal, 0; mild, 1; moderate, 2; and severe, 3 14,15. The participants were categorized into four groups according to the steatosis grade determined by abdominal ultrasonography and body mass index (BMI) z-score based on the 2017 Korean National Growth Chart for children and adolescents 16: healthy control (HC), steatosis grade = 0 and BMI z-score ≤ 1; lean NAFLD (LN), steatosis grade ≥ 1 and BMI z-score ≤ 1; overweight control (OC), steatosis grade = 0 and BMI z-score > 1; and overweight NAFLD (ON), steatosis grade ≥ 1 and BMI z-score > 1.","TREATMENT":"Observational"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"frozen plasma samples were thawed on ice and vortexed, followed by centrifugation at 2,750 × g, 4℃ for 5 min before the samples were loaded onto a 96-well plate with a filter. After the addition of 10 μL of analytical and pooled plasma samples and calibration standards to each well, the plates were dried with a nitrogen evaporator and derivatized with phenyl isothiocyanate. Then, dried samples were extracted with ammonium acetate solution in methanol and aliquoted into two deep-well plates for liquid chromatography mode and flow injection analysis (FIA) mode (described in the manual), followed by dilution with water and an FIA solvent, respectively. Both deep-well plates were placed in an autosampler of Ultimate 3000 ultra-performance liquid chromatography coupled with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, MA, USA) and analyzed using the validated method.","SAMPLEPREP_PROTOCOL_FILENAME":"UM-p400-HR-Thermo-3.pdf","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"4℃"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"FIA2 method for analysis of acylcarnitines For more details, please refer sections 4.6, 4.7, 5, 9, 10.1, and 10.2 of the method file attached.","METHODS_FILENAME":"UM-p400-HR-Thermo-3.pdf","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"NA","SOLVENT_A":"290mL Methanol + 1 ampule FIA mobile phase additive","CHROMATOGRAPHY_TYPE":"None (Direct infusion)"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"UM-p400-HR-Thermo-3.pdf","ACQUISITION_PARAMETERS_FILE":"UM-p400-HR-Thermo-3.pdf","PROCESSING_PARAMETERS_FILE":"UM-MetIDQ-Oxygen-9.pdf","DATA_FORMAT":".raw"}, "MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"MS acquisition method, data processing method and software used for feature assignments are described in analysis protocol file attached. Please refer sections 10.3 (MS acquisition parameters) and 5.3 (data processing) of the method file attached. The final quantitative results were exported to micromolar values with pooled quality control sample normalization by median. Subsequently, values under the lower limit of detection were imputed by one-fifth of the minimum positive values of their corresponding variables. These data were used for further analysis.","ION_MODE":"POSITIVE"}, "MS_METABOLITE_DATA":{ "Units":"μM", 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