Summary of Study ST003520

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 PR002165. The data can be accessed directly via it's Project DOI: 10.21228/M8S247 This work is supported by NIH grant, U2C- DK119886.

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Study IDST003520
Study TitleIdentification of Plasma Metabolomic Biomarkers of Juvenile Idiopathic Arthritis
Study TypeClinical
Study SummaryThis study utilizes plasma metabolomic profiling to identify biomarkers associated with juvenile idiopathic arthritis (JIA) by analyzing samples from treatment-naïve JIA patients and non-JIA controls. Significant metabolic alterations were detected, with sphingosine metabolites and fatty acid ethanolamides showing notable increases in JIA patients, while specific compounds such as sarcosine were decreased. The research highlights 11 highly discriminatory metabolites, including sphinganine-1-phosphate, demonstrating potential for improved JIA diagnosis and treatment through targeted metabolic profiling.
Institute
University of Kansas
DepartmentCenter for Computational Biology
LaboratoryFunk
Last NameKumar
First NameAmar
AddressMultidisciplinary Research Bldg. 2030 Becker Drive Lawrence, KS 66047
Emailamarkumar@ku.edu
Phone18723016225
Submit Date2024-09-09
Num Groups2
Total Subjects210
Num Males82
Num Females128
Study CommentsAlthough the raw dataset initially included 210 subjects, only 207 were included in the final analysis due to consent-related exclusions. These three subjects were removed to ensure compliance with ethical standards.
Analysis Type DetailLC-MS
Release Date2024-11-01
Release Version1
Amar Kumar Amar Kumar
https://dx.doi.org/10.21228/M8S247
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002165
Project DOI:doi: 10.21228/M8S247
Project Title:Identification of Plasma Metabolomic Biomarkers of Juvenile Idiopathic Arthritis
Project Type:Clinical
Project Summary:The identification of reliable disease and therapeutic biomarkers remains a significant challenge for early diagnosis and the initiation of effective disease-modifying therapies in juvenile idiopathic arthritis (JIA). In this study, comprehensive plasma metabolomic profiling was conducted to elucidate metabolic biomarkers associated with JIA pathophysiology.
Institute:University of Kansas
Department:Center for Computational Biology
Laboratory:Funk
Last Name:Kumar
First Name:Amar
Address:Multidisciplinary Research Bldg. 2030 Becker Drive, Lawrence, KS 66047
Email:amarkumar@ku.edu
Phone:18723016225

Subject:

Subject ID:SU003649
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:1.50–20.33 years
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Group
SA386516UKAN-00680Crohn's Disease
SA386517UKAN-00636Crohn's Disease
SA386518UKAN-00637Crohn's Disease
SA386519UKAN-00642Crohn's Disease
SA386520UKAN-00643Crohn's Disease
SA386521UKAN-00645Crohn's Disease
SA386522UKAN-00670Crohn's Disease
SA386523UKAN-00671Crohn's Disease
SA386524UKAN-00674Crohn's Disease
SA386525UKAN-00675Crohn's Disease
SA386526UKAN-00677Crohn's Disease
SA386527UKAN-00683Crohn's Disease
SA386528UKAN-00633Crohn's Disease
SA386529UKAN-00684Crohn's Disease
SA386530UKAN-00686Crohn's Disease
SA386531UKAN-00710Crohn's Disease
SA386532UKAN-00714Crohn's Disease
SA386533UKAN-00715Crohn's Disease
SA386534UKAN-00716Crohn's Disease
SA386535UKAN-00721Crohn's Disease
SA386536UKAN-00723Crohn's Disease
SA386537UKAN-00724Crohn's Disease
SA386538UKAN-00725Crohn's Disease
SA386539UKAN-00635Crohn's Disease
SA386540UKAN-00712Crohn's Disease
SA386541UKAN-00631Crohn's Disease
SA386542UKAN-00632Healthy_Control
SA386543UKAN-00827Healthy_Control
SA386544UKAN-00708Healthy_Control
SA386545UKAN-00707Healthy_Control
SA386546UKAN-00822Healthy_Control
SA386547UKAN-00823Healthy_Control
SA386548UKAN-00824Healthy_Control
SA386549UKAN-00825Healthy_Control
SA386550UKAN-00826Healthy_Control
SA386551UKAN-00829Healthy_Control
SA386552UKAN-00828Healthy_Control
SA386553UKAN-00711Healthy_Control
SA386554UKAN-00830Healthy_Control
SA386555UKAN-00831Healthy_Control
SA386556UKAN-00832Healthy_Control
SA386557UKAN-00833Healthy_Control
SA386558UKAN-00685Healthy_Control
SA386559UKAN-00682Healthy_Control
SA386560UKAN-00681Healthy_Control
SA386561UKAN-00709Healthy_Control
SA386562UKAN-00717Healthy_Control
SA386563UKAN-00713Healthy_Control
SA386564UKAN-00801Healthy_Control
SA386565UKAN-00793Healthy_Control
SA386566UKAN-00794Healthy_Control
SA386567UKAN-00795Healthy_Control
SA386568UKAN-00796Healthy_Control
SA386569UKAN-00797Healthy_Control
SA386570UKAN-00798Healthy_Control
SA386571UKAN-00799Healthy_Control
SA386572UKAN-00800Healthy_Control
SA386573UKAN-00802Healthy_Control
SA386574UKAN-00678Healthy_Control
SA386575UKAN-00803Healthy_Control
SA386576UKAN-00804Healthy_Control
SA386577UKAN-00726Healthy_Control
SA386578UKAN-00634Healthy_Control
SA386579UKAN-00722Healthy_Control
SA386580UKAN-00720Healthy_Control
SA386581UKAN-00719Healthy_Control
SA386582UKAN-00718Healthy_Control
SA386583UKAN-00679Healthy_Control
SA386584UKAN-00834Healthy_Control
SA386585UKAN-00853Healthy_Control
SA386586UKAN-00864Healthy_Control
SA386587UKAN-00854Healthy_Control
SA386588UKAN-00676Healthy_Control
SA386589UKAN-00852Healthy_Control
SA386590UKAN-00856Healthy_Control
SA386591UKAN-00857Healthy_Control
SA386592UKAN-00858Healthy_Control
SA386593UKAN-00859Healthy_Control
SA386594UKAN-00860Healthy_Control
SA386595UKAN-00861Healthy_Control
SA386596UKAN-00862Healthy_Control
SA386597UKAN-00855Healthy_Control
SA386598UKAN-00646Healthy_Control
SA386599UKAN-00863Healthy_Control
SA386600UKAN-00667Healthy_Control
SA386601UKAN-00668Healthy_Control
SA386602UKAN-00630Healthy_Control
SA386603UKAN-00629Healthy_Control
SA386604UKAN-00638Healthy_Control
SA386605UKAN-00673Healthy_Control
SA386606UKAN-00639Healthy_Control
SA386607UKAN-00640Healthy_Control
SA386608UKAN-00672Healthy_Control
SA386609UKAN-00641Healthy_Control
SA386610UKAN-00628Healthy_Control
SA386611UKAN-00627Healthy_Control
SA386612UKAN-00644Healthy_Control
SA386613UKAN-00669Healthy_Control
SA386614UKAN-00808JIA
SA386615UKAN-00809JIA
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Collection:

Collection ID:CO003642
Collection Summary:EDTA (Ethylenediaminetetraacetic acid) plasma specimens were systematically harvested from distinct patient cohorts under uniform preservative protocols and collection methodologies, although executed across disparate facilities by varying technical staff. The bio-samples involved two primary groups: patients diagnosed with Juvenile Idiopathic Arthritis (JIA) prior to the initiation of disease-modifying antirheumatic drugs (DMARDs), and a reference non-JIA pediatric population including children with active Crohn’s disease and healthy controls without autoimmune or discernible gastrointestinal or rheumatologic pathology. For JIA, plasma samples were procured in two phases: the discovery cohort consisting of 60 subjects from Children’s Mercy Kansas City (CM-KC), and the replication cohort comprising 49 subjects enrolled through PROMOTE studies at both CM-KC and Cincinnati Children’s Hospital Medical Center (CCHMC), Ohio. The non-JIA samples (n = 98) were sourced from a biorepository at CM-KC, collected in a fasted state during morning hours (7:30–11:30 A.M.), and were all from subjects who were age-matched to the JIA group and showed no organic causes for gastrointestinal symptoms, including no significant findings on histopathology from tissues biopsied during endoscopy. All specimens at CM-KC were gathered from subjects who had fasted for at least 8 hours, ensuring consistency in sample conditions. Patients provided age-appropriate informed consent or assent, and all sample collections were conducted under IRB-approved protocols to uphold ethical standards in research. Upon receiving, the venous blood samples were centrifuged using a Beckman tabletop centrifuge at 2000 RPM for 10 minutes to separate plasma. The resultant plasma supernatant was then aliquoted and preserved at -80°C. Prior to undergoing global metabolomic analysis, these samples were shipped on dry ice. Please note that for the analysis, both the datasets were combined into one dataset i.e., merged dataset, for more information please refer to the manuscript. DOI : https://doi.org/10.3390/metabo14090499
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003658
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003656
Sampleprep Summary:Samples were thawed on ice prior to extraction. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. In order to dissociate small molecules bound to or trapped in proteins, lysate was precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into multiple fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and remaining fractions reserved for backup. Samples were dried under warm nitrogen to remove the organic solvent. The sample extracts were stored sealed at -80C if not analysed immediately
Processing Storage Conditions:-80℃

Chromatography:

Chromatography ID:CH004385
Chromatography Summary:Low pH polar (LC/MS Pos early)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5
Solvent B:100% methanol; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH004386
Chromatography Summary:Low pH Lipophilic (LC/MS Pos late)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:0.60 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5
Solvent B:50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH004387
Chromatography Summary:High pH (LC/MS Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:0.35 mL/min
Solvent A:100% water; 6.5 mM ammonium bicarbonate, pH 8
Solvent B:95% methanol/5% water; 6.5 mM ammonium bicarbonate
Chromatography Type:Reversed phase
  
Chromatography ID:CH004388
Chromatography Summary:HILIC (LC/MS Polar Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:0.50 mL/min
Solvent A:15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with ammonium hydroxide)
Solvent B:50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with ammonium hydroxide)
Chromatography Type:HILIC

Analysis:

Analysis ID:AN005778
Analysis Type:MS
Chromatography ID:CH004385
Num Factors:3
Num Metabolites:274
Units:Peak area
  
Analysis ID:AN005779
Analysis Type:MS
Chromatography ID:CH004386
Num Factors:3
Num Metabolites:241
Units:Peak area
  
Analysis ID:AN005780
Analysis Type:MS
Chromatography ID:CH004387
Num Factors:3
Num Metabolites:311
Units:Peak area
  
Analysis ID:AN005781
Analysis Type:MS
Chromatography ID:CH004388
Num Factors:3
Num Metabolites:105
Units:Peak area
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