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

Select appropriate tab below to view additional metadata details:

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
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Clinical group
SA343316NEG_744_re-
SA343317NEG_740_re-
SA343318NEG_760_re-
SA343319NEG_770_re-
SA343320NEG_787_re-
SA343321NEG_734_re-
SA343322NEG_769_re-
SA343323NEG_732_re-
SA343324NEG_714_re-
SA343325NEG_711_re-
SA343326NEG_717_re-
SA343327NEG_721_re-
SA343328NEG_800_re-
SA343329NEG_731_re-
SA343330NEG_733_re-
SA343331NEG_808_re-
SA343332NEG_870_re-
SA343333NEG_862_re-
SA343334NEG_876_re-
SA343335NEG_885_re-
SA343336NEG_893_re-
SA343337NEG_888_re-
SA343338NEG_855_re-
SA343339NEG_845_re-
SA343340NEG_814_re-
SA343341NEG_707_re-
SA343342NEG_823_re-
SA343343NEG_828_re-
SA343344NEG_836_re-
SA343345NEG_831_re-
SA343346NEG_802_re-
SA343347NEG_693_re-
SA343348NEG_619_re-
SA343349NEG_616_re-
SA343350NEG_624_re-
SA343351NEG_629_re-
SA343352NEG_632_re-
SA343353NEG_631_re-
SA343354NEG_614_re-
SA343355NEG_611_re-
SA343356NEG_580_re-
SA343357NEG_577_re-
SA343358NEG_585_re-
SA343359NEG_586_re-
SA343360NEG_606_re-
SA343361NEG_596_re-
SA343362NEG_633_re-
SA343363NEG_634_re-
SA343364NEG_680_re-
SA343365NEG_678_re-
SA343366NEG_686_re-
SA343367NEG_687_re-
SA343368NEG_896_re-
SA343369NEG_688_re-
SA343370NEG_677_re-
SA343371NEG_674_re-
SA343372NEG_641_re-
SA343373NEG_638_re-
SA343374NEG_650_re-
SA343375NEG_657_re-
SA343376NEG_669_re-
SA343377NEG_665_re-
SA343378NEG_701_re-
SA343379NEG_901_re-
SA343380QC32-
SA343381QC31-
SA343382QC33-
SA343383QC34-
SA343384QC36-
SA343385QC35-
SA343386QC30-
SA343387QC29-
SA343388QC24-
SA343389QC23-
SA343390QC25-
SA343391QC26-
SA343392QC28-
SA343393QC27-
SA343394QC37-
SA343395QC38-
SA343396QC48-
SA343397QC47-
SA343398QC49-
SA343399QC50-
SA343400QC52-
SA343401QC51-
SA343402QC46-
SA343403QC45-
SA343404QC40-
SA343405QC39-
SA343406QC41-
SA343407QC42-
SA343408QC44-
SA343409QC43-
SA343410QC22-
SA343411QC21-
SA343412QC1-
SA343413POS_582_re-
SA343414QC2-
SA343415QC3-
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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.

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

Analysis:

Analysis ID:AN005215
Analysis Type:MS
Chromatography ID:CH003944
Num Factors:8
Num Metabolites:102
Rt Units:Minutes
Units:peak area
  
Analysis ID:AN005216
Analysis Type:MS
Chromatography ID:CH003944
Num Factors:8
Num Metabolites:120
Rt Units:Minutes
Units:Peak area
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