Summary of Study ST003177

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 PR001976. The data can be accessed directly via it's Project DOI: 10.21228/M89J06 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 IDST003177
Study TitleA Longitudinal Study in Rheumatoid Arthritis Unveils Metabolomic Biomarkers Preceding Clinical Onset, Assessing Disease Severity, and Anticipating Treatment Response to csDMARDs
Study SummaryRheumatoid arthritis (RA) is a bundle of systemic inflammatory diseases mainly affecting the joints, complicating the identification of biomarkers for early diagnosis, predicting disease progress and therapeutic outcomes. This study scrutinizes a longitudinal cohort of RA, inclusive of follow-ups, alongside OA, UA and ACPA/RF-RA and healthy controls, aiming to discover plasma metabolic markers that can precede RA onset, assess disease activity, and forecast treatment efficacy. Our investigation revealed substantial metabolic alterations at both the pathway and individual metabolite levels across RA, at-risk or RA and healthy control. The drug response predictive models constructed on critical differential metaboites showed optimal performance. Additionally, our longitudinal data sheds light on the molecular impacts on metabolism of csDMARDs in RA.
Institute
West China Hospital of Sichuan University
Last NameZhu
First NameChenxi
AddressWest China Hospital, Sichuan University, 37# Guoxue Xiang, Chengdu, Sichuan, 610041, China.
Emailchenxizhu1995@gmail.com
Phone+8615026603760
Submit Date2024-04-12
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-05-11
Release Version1
Chenxi Zhu Chenxi Zhu
https://dx.doi.org/10.21228/M89J06
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001976
Project DOI:doi: 10.21228/M89J06
Project Title:A Longitudinal Study in Rheumatoid Arthritis Unveils Metabolomic Biomarkers Preceding Clinical Onset, Assessing Disease Severity, and Anticipating Treatment Response to csDMARDs
Project Summary:Rheumatoid arthritis (RA) is a bundle of systemic inflammatory diseases mainly affecting the joints, complicating the identification of biomarkers for early diagnosis, predicting disease progress and therapeutic outcomes. This study scrutinizes a longitudinal cohort of RA, inclusive of follow-ups, alongside OA, UA and ACPA/RF-RA and healthy controls, aiming to discover plasma metabolic markers that can precede RA onset, assess disease activity, and forecast treatment efficacy. Our investigation revealed substantial metabolic alterations at both the pathway and individual metabolite levels across RA, at-risk or RA and healthy control. The drug response predictive models constructed on critical differential metaboites showed optimal performance. Additionally, our longitudinal data sheds light on the molecular impacts on metabolism of csDMARDs in RA.
Institute:Department of Rheumatology and Immunology, West China Hospital,Sichuan University, Chengdu, Sichuan, China
Last Name:Zhu
First Name:Chenxi
Address:West China Hospital, Sichuan University, 37# Guoxue Xiang, Chengdu, Sichuan, 610041, China., Chengdu, Sichuan, 610065, China
Email:chenxizhu1995@gmail.com
Phone:+86 150 2660 3760

Subject:

Subject ID:SU003296
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Clinical group Sample source
SA343818NEG_140CCP-RA blood
SA343819POS_475CCP-RA blood
SA343820NEG_226CCP-RA blood
SA343821NEG_560CCP-RA blood
SA343822POS_637CCP-RA blood
SA343823POS_226CCP-RA blood
SA343824POS_987CCP-RA blood
SA343825POS_140CCP-RA blood
SA343826POS_472CCP-RA blood
SA343827NEG_475CCP-RA blood
SA343828NEG_464CCP-RA blood
SA343829NEG_461CCP-RA blood
SA343830POS_980CCP-RA blood
SA343831POS_310CCP-RA blood
SA343832POS_560CCP-RA blood
SA343833NEG_980CCP-RA blood
SA343834NEG_472CCP-RA blood
SA343835NEG_987CCP-RA blood
SA343836POS_464CCP-RA blood
SA343837NEG_310CCP-RA blood
SA343838POS_461CCP-RA blood
SA343839NEG_637CCP-RA blood
SA345220NEG_942health blood
SA345221POS_113health blood
SA345222POS_624health blood
SA345223POS_17health blood
SA345224POS_109health blood
SA345225POS_281health blood
SA345226POS_942health blood
SA345227POS_279health blood
SA345228POS_915health blood
SA345229NEG_965health blood
SA345230POS_923health blood
SA345231POS_947health blood
SA345232POS_931health blood
SA345233POS_11health blood
SA345234POS_619health blood
SA345235NEG_958health blood
SA345236POS_611health blood
SA345237POS_605health blood
SA345238NEG_961health blood
SA345239NEG_947health blood
SA345240POS_548health blood
SA345241POS_991health blood
SA345242POS_621health blood
SA345243POS_926health blood
SA345244POS_550health blood
SA345245POS_733health blood
SA345246POS_111health blood
SA345247NEG_977health blood
SA345248POS_976health blood
SA345249POS_540health blood
SA345250POS_975health blood
SA345251POS_974health blood
SA345252POS_973health blood
SA345253POS_977health blood
SA345254NEG_902health blood
SA345255POS_105health blood
SA345256POS_719health blood
SA345257POS_541health blood
SA345258NEG_11health blood
SA345259POS_288health blood
SA345260POS_726health blood
SA345261POS_972health blood
SA345262POS_724health blood
SA345263POS_965health blood
SA345264POS_722health blood
SA345265POS_580health blood
SA345266NEG_33health blood
SA345267POS_967health blood
SA345268POS_577health blood
SA345269NEG_17health blood
SA345270POS_971health blood
SA345271POS_970health blood
SA345272POS_720health blood
SA345273NEG_26health blood
SA345274POS_542health blood
SA345275POS_728health blood
SA345276NEG_974health blood
SA345277NEG_973health blood
SA345278NEG_975health blood
SA345279NEG_976health blood
SA345280NEG_926health blood
SA345281NEG_931health blood
SA345282NEG_972health blood
SA345283NEG_967health blood
SA345284POS_545health blood
SA345285NEG_970health blood
SA345286NEG_971health blood
SA345287POS_732health blood
SA345288POS_629health blood
SA345289NEG_923health blood
SA345290POS_285health blood
SA345291POS_543health blood
SA345292NEG_991health blood
SA345293POS_982health blood
SA345294POS_981health blood
SA345295NEG_915health blood
SA345296POS_983health blood
SA345297NEG_982health blood
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Collection:

Collection ID:CO003289
Collection Summary:The study collected plasma samples from all participants at West China Hospital, Sichuan University. These were approved by the Research Ethics Committee of West China Hospital, Sichuan University (Permission number: 2021(790)), and informed consent was obtained from all participants. Patients were diagnosed with RA according to the 2010 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) criteria. The healthy control group consisted of individuals matched in age and gender, with no history or clinical evidence of autoimmune or rheumatic diseases. Blood collection followed standard venipuncture procedures using anticoagulant tubes. Plasma samples were obtained after centrifugation and stored at -80°C. ACPA levels were measured using Elecsys anti-CCP detection on the Cobas® e 801 module (Roche Diagnostics, Mannheim, Germany), with results categorized as positive (≥17.0 U/ml) or negative (<17.0 U/ml).
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR003305
Treatment Summary:A subset of RA patients were followed-up for three months after treatment with MTX monotherapy or a combination of csDMARDs. During this period, clinical data and blood specimens were gathered at the conclusion.

Sample Preparation:

Sampleprep ID:SP003303
Sampleprep Summary:The plasma samples were thawed by transferring them from -80°C to a 4°C refrigerator. Then, take out 50 μL of the plasma sample into another tube after vortex mixing and added to 250 μL of pre-cooled Spike MeOH containing isotopic chemicals (120.89 μM 13C6-D-glucose, 23.12 mM 13C5-L-glutamate-15N). The mixture was thoroughly mixed by vortexing at 1500 rpm for 2 minutes at 4°C. The mixture was then placed in a -20°C refrigerator and allowed to stand for 30 minutes. Afterward, ultrasonication was performed in an ice-water bath for 10 minutes. Following ultrasonication, the mixture was centrifuged at 13,000 rpm for 20 minutes at 4°C. 20 μL of each sample from every batch was extracted from the tube and mixed for QC analysis using mass spectrometry (MS). The 150ul remaining extract was concentrated, vacuum dried, and stored at -80°C.

Combined analysis:

Analysis ID AN005215 AN005216
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system SCIEX ExionLC UHPLC SCIEX ExionLC UHPLC
Column Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex Triple Quad 5500+ ABI Sciex Triple Quad 5500+
Ion Mode POSITIVE NEGATIVE
Units peak area Peak area

Chromatography:

Chromatography ID:CH003944
Chromatography Summary:SCIEX ExionLC UHPLC system coupled with a SCIEX Triple Quad 5500+ LC-MS/MS
Instrument Name:SCIEX ExionLC UHPLC
Column Name:Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
Column Temperature:40°C
Flow Gradient:1.5 min, 90% B; 5 min, 45% B; 10 min, 45% B; 12 min, 90% B; 25 min, 90% B
Flow Rate:0.3 mL/min
Solvent A:90% water/10% acetonitrile; 10 mM ammonium acetate; 0.2% acetic acid
Solvent B:90% acetonitrile/10% water; 10 mM ammonium acetate; 0.2% acetic acid
Chromatography Type:HILIC

MS:

MS ID:MS004948
Analysis ID:AN005215
Instrument Name:ABI Sciex Triple Quad 5500+
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Within each batch, normalization was performed by dividing the level of each metabolite by the average value of the first and last QC samples in that batch. Subsequently, a cross-sample total sum correction was conducted for all metabolites. Then, the data was mean-centered and divided by the standard deviation of each variable for standardization. Finally, a log10 transformation was applied to the data. We further removed metabolites with a coefficient of variation (CV) greater than 0.35 and any metabolites with more than 50% missing values within any group (RA, at-risk of RA, and Health). For analyses intolerant to missing data, any missing values are substituted with 1/5 of the minimum positive value of their corresponding variables.
Ion Mode:POSITIVE
  
MS ID:MS004949
Analysis ID:AN005216
Instrument Name:ABI Sciex Triple Quad 5500+
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Within each batch, normalization was performed by dividing the level of each metabolite by the average value of the first and last QC samples in that batch. Subsequently, a cross-sample total sum correction was conducted for all metabolites. Then, the data was mean-centered and divided by the standard deviation of each variable for standardization. Finally, a log10 transformation was applied to the data. We further removed metabolites with a coefficient of variation (CV) greater than 0.35 and any metabolites with more than 50% missing values within any group (RA, at-risk of RA, and Health). For analyses intolerant to missing data, any missing values are substituted with 1/5 of the minimum positive value of their corresponding variables.
Ion Mode:NEGATIVE
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