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

Select appropriate tab below to view additional metadata details:

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

Factors:

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

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

Combined analysis:

Analysis ID AN005778 AN005779 AN005780 AN005781
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units Peak area Peak area Peak area Peak area

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

MS:

MS ID:MS005498
Analysis ID:AN005778
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Pos early) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations.
Ion Mode:POSITIVE
  
MS ID:MS005499
Analysis ID:AN005779
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Pos late) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations.
Ion Mode:POSITIVE
  
MS ID:MS005500
Analysis ID:AN005780
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Neg) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations.
Ion Mode:NEGATIVE
  
MS ID:MS005501
Analysis ID:AN005781
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Polar) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations.
Ion Mode:NEGATIVE
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