Summary of Study ST002269

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001451. The data can be accessed directly via it's Project DOI: 10.21228/M85H8N This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002269
Study TitleTargeted plasma metabolomics in pediatric NAFLD patients
Study SummarySeveral 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
DepartmentDepartment of Clinical Pharmacology and Therapeutics
Last NameChae
First NameWoori
Address101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
Emailyunus@snu.ac.kr
Phone82-2-740-8905
Submit Date2022-08-07
Num Groups4
Total Subjects165
Num Males122
Num Females43
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS/MS(Dir. Inf.)
Release Date2023-08-07
Release Version1
Woori Chae Woori Chae
https://dx.doi.org/10.21228/M85H8N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001451
Project DOI:doi: 10.21228/M85H8N
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]

Subject:

Subject ID:SU002355
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.

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA217562H_C_243Healthy Control
SA217563H_C_245Healthy Control
SA217564H_C_248Healthy Control
SA217565H_C_240Healthy Control
SA217566H_C_237Healthy Control
SA217567H_C_235Healthy Control
SA217568H_C_236Healthy Control
SA217569H_C_251Healthy Control
SA217570H_C_238Healthy Control
SA217571H_C_254Healthy Control
SA217572H_C_259Healthy Control
SA217573H_O_111Healthy Control
SA217574H_C_203Healthy Control
SA217575H_C_258Healthy Control
SA217576H_C_257Healthy Control
SA217577H_C_234Healthy Control
SA217578H_C_255Healthy Control
SA217579H_C_256Healthy Control
SA217580H_C_253Healthy Control
SA217581H_C_249Healthy Control
SA217582H_C_211Healthy Control
SA217583H_C_212Healthy Control
SA217584H_C_213Healthy Control
SA217585H_C_209Healthy Control
SA217586H_C_208Healthy Control
SA217587H_C_205Healthy Control
SA217588H_C_232Healthy Control
SA217589H_C_206Healthy Control
SA217590H_C_215Healthy Control
SA217591H_C_214Healthy Control
SA217592H_C_216Healthy Control
SA217593H_C_224Healthy Control
SA217594H_C_230Healthy Control
SA217595H_C_231Healthy Control
SA217596H_C_221Healthy Control
SA217597H_C_223Healthy Control
SA217598H_C_218Healthy Control
SA217599H_C_204Healthy Control
SA217600H_C_217Healthy Control
SA217601S_N_1161Lean NAFLD
SA217602S_N_L2Lean NAFLD
SA217603H_N_125Lean NAFLD
SA217604S_N_L6Lean NAFLD
SA217605H_N_024Lean NAFLD
SA217606H_N_051Lean NAFLD
SA217607H_N_101Lean NAFLD
SA217608H_N_057Lean NAFLD
SA217609H_N_096Lean NAFLD
SA217610H_O_242Obese Control
SA217611H_O_244Obese Control
SA217612H_O_229Obese Control
SA217613H_O_247Obese Control
SA217614H_O_241Obese Control
SA217615H_O_260Obese Control
SA217616H_O_228Obese Control
SA217617H_O_261Obese Control
SA217618H_O_252Obese Control
SA217619H_O_250Obese Control
SA217620H_O_225Obese Control
SA217621H_C_246Obese Control
SA217622H_O_013Obese Control
SA217623H_C_239Obese Control
SA217624H_O_226Obese Control
SA217625H_C_220Obese Control
SA217626H_O_161Obese Control
SA217627H_C_233Obese Control
SA217628H_O_222Obese Control
SA217629H_O_207Obese Control
SA217630H_O_219Obese Control
SA217631H_O_210Obese Control
SA217632H_N_119Obese NAFLD
SA217633H_N_117Obese NAFLD
SA217634H_N_116Obese NAFLD
SA217635H_N_124Obese NAFLD
SA217636H_N_118Obese NAFLD
SA217637H_N_121Obese NAFLD
SA217638H_N_115Obese NAFLD
SA217639H_N_123Obese NAFLD
SA217640H_N_122Obese NAFLD
SA217641H_N_120Obese NAFLD
SA217642H_N_108Obese NAFLD
SA217643H_N_105Obese NAFLD
SA217644H_N_106Obese NAFLD
SA217645H_N_104Obese NAFLD
SA217646H_N_103Obese NAFLD
SA217647H_N_102Obese NAFLD
SA217648H_N_107Obese NAFLD
SA217649H_N_126Obese NAFLD
SA217650H_N_113Obese NAFLD
SA217651H_N_112Obese NAFLD
SA217652H_N_110Obese NAFLD
SA217653H_N_109Obese NAFLD
SA217654H_N_114Obese NAFLD
SA217655H_N_133Obese NAFLD
SA217656S_N_L15Obese NAFLD
SA217657S_N_L14Obese NAFLD
SA217658S_N_L13Obese NAFLD
SA217659S_N_L11Obese NAFLD
SA217660S_N_L3Obese NAFLD
SA217661S_N_L4Obese NAFLD
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Collection:

Collection ID:CO002348
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 ID:TR002367
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

Sample Preparation:

Sampleprep ID:SP002361
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℃

Combined analysis:

Analysis ID AN003706 AN003707 AN003708 AN003709
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase None (Direct infusion) None (Direct infusion)
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Biocrates AbsoluteIDQ p400 HR Kit UHPLC (PN 9120052121032) Biocrates AbsoluteIDQ p400 HR Kit UHPLC (PN 9120052121032) NA NA
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE POSITIVE POSITIVE POSITIVE
Units μM μM μM μM

Chromatography:

Chromatography ID:CH002745
Chromatography Summary:LC1 method for analysis of amino acids and biogenic amines 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:Biocrates AbsoluteIDQ p400 HR Kit UHPLC (PN 9120052121032)
Column Temperature:50
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile; 0.2% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH002746
Chromatography Summary:LC2 method for analysis of isoleucine 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:Biocrates AbsoluteIDQ p400 HR Kit UHPLC (PN 9120052121032)
Column Temperature:50
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile; 0.2% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH002747
Chromatography Summary:FIA1 method for analysis of acylcarnitines and lipids 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)
  
Chromatography ID:CH002748
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)

MS:

MS ID:MS003455
Analysis ID:AN003706
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 9 (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
Acquisition Parameters File:UM-p400-HR-Thermo-3.pdf
Processing Parameters File:UM-p400-HR-Thermo-3.pdf
Analysis Protocol File:UM-p400-HR-Thermo-3.pdf
  
MS ID:MS003456
Analysis ID:AN003707
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 9 (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
Acquisition Parameters File:UM-p400-HR-Thermo-3.pdf
Processing Parameters File:UM-p400-HR-Thermo-3.pdf
Analysis Protocol File:UM-p400-HR-Thermo-3.pdf
  
MS ID:MS003457
Analysis ID:AN003708
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
Acquisition Parameters File:UM-p400-HR-Thermo-3.pdf
Processing Parameters File:UM-MetIDQ-Oxygen-9.pdf
Analysis Protocol File:UM-p400-HR-Thermo-3.pdf
  
MS ID:MS003458
Analysis ID:AN003709
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
Acquisition Parameters File:UM-p400-HR-Thermo-3.pdf
Processing Parameters File:UM-MetIDQ-Oxygen-9.pdf
Analysis Protocol File:UM-p400-HR-Thermo-3.pdf
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