Summary of Study ST001949

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 PR001236. The data can be accessed directly via it's Project DOI: 10.21228/M8Z10X This work is supported by NIH grant, U2C- DK119886.

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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 IDST001949
Study TitlePlasma Metabolome Normalization in Rheumatoid Arthritis following initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy
Study TypeClinical
Study SummaryMethotrexate (MTX) efficacy in the treatment of rheumatoid arthritis (RA) is variable and unpredictable, resulting in a need to identify biomarkers to guide drug therapy. This study evaluates changes in the plasma metabolome associated with response to MTX in RA with the goal of understanding the metabolic basis for MTX efficacy towards the identification of potential metabolic biomarkers of MTX response.
Institute
University of Kansas
DepartmentPharmacy Practice
LaboratoryFunk
Last NameMedcalf
First NameMatthew
Address2106 Olathe Boulevard
Emailmmedcalf@ku.edu
Phone13147880236
Submit Date2021-10-20
Num Groups3
Total Subjects40
Num Males9
Num Females31
Raw Data AvailableYes
Analysis Type DetailGC-MS
Release Date2022-11-07
Release Version1
Matthew Medcalf Matthew Medcalf
https://dx.doi.org/10.21228/M8Z10X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001236
Project DOI:doi: 10.21228/M8Z10X
Project Title:Plasma Metabolome Normalization in Rheumatoid Arthritis following initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy
Project Type:Clinical
Project Summary:Methotrexate (MTX) efficacy in the treatment of rheumatoid arthritis (RA) is variable and unpredictable, resulting in a need to identify biomarkers to guide drug therapy. This study evaluates changes in the plasma metabolome associated with response to MTX in RA with the goal of understanding the metabolic basis for MTX efficacy towards the identification of potential metabolic biomarkers of MTX response.
Institute:University of Kansas
Department:Pharmacy Practice
Laboratory:Funk
Last Name:Medcalf
First Name:Matthew
Address:2106 Olathe Boulevard
Email:mmedcalf@ku.edu
Phone:13147880236
Funding Source:KL2TR002367

Subject:

Subject ID:SU002027
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:21 - 84
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Condition
SA18386415_015Control
SA18386514_014Control
SA18386616_016Control
SA18386713_013Control
SA18386819_019Control
SA1838691_001Control
SA18387020_020Control
SA18387112_012Control
SA18387218_018Control
SA18387317_017Control
SA1838744_004Control
SA1838753_003Control
SA18387611_011Control
SA1838772_002Control
SA1838786_006Control
SA1838795_005Control
SA1838809_009Control
SA1838818_008Control
SA1838827_007Control
SA18388310_010Control
SA18388445_045RA
SA18388543_043RA
SA18388639_039RA
SA18388747_047RA
SA18388837_037RA
SA18388941_041RA
SA18389057_057RA
SA18389159_059RA
SA18389235_035RA
SA18389355_055RA
SA18389453_053RA
SA18389551_051RA
SA18389649_049RA
SA18389731_031RA
SA18389825_025RA
SA18389927_027RA
SA18390029_029RA
SA18390123_023RA
SA18390233_033RA
SA18390321_021RA
SA18390454_054RA+MTX
SA18390552_052RA+MTX
SA18390660_060RA+MTX
SA18390724_024RA+MTX
SA18390858_058RA+MTX
SA18390926_026RA+MTX
SA18391056_056RA+MTX
SA18391122_022RA+MTX
SA18391248_048RA+MTX
SA18391332_032RA+MTX
SA18391440_040RA+MTX
SA18391538_038RA+MTX
SA18391634_034RA+MTX
SA18391742_042RA+MTX
SA18391830_030RA+MTX
SA18391936_036RA+MTX
SA18392028_028RA+MTX
SA18392146_046RA+MTX
SA18392244_044RA+MTX
SA18392350_050RA+MTX
Showing results 1 to 60 of 60

Collection:

Collection ID:CO002020
Collection Summary:Venous blood samples were collected in 8.5 mL ACD Solution A BD Vacutainer tubes for the healthy control, and RA patients prior to initiation of MTX and at a 16 week follow up visit. Venous blood samples were collected and separated into plasma and cellular fractions by centrifugation at 3,000 RPM in a Thermo Scientific Sorvall Legend XTR centrifuge for 10 minutes. The resulting plasma supernatant was separated into aliquots and stored at -80 ⁰C prior to analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃
Additives:ACD

Treatment:

Treatment ID:TR002039
Treatment Summary:Biobanked plasma samples were acquired from a subset of RA patients (n=20) that participated in a 16-week multicenter open-label study that sought to evaluated predictors of MTX response in RA (ClinicalTrials.gov NCT03414502) (PMID: 32911284). The study included sites within the Rheumatology Arthritis Investigational Network (RAIN). For each patient, plasma samples at baseline and 16-weeks were provided for analysis. All patients received 15 mg/week of MTX and 1 mg/day of folic acid upon enrollment. The MTX does was escalated to 20 mg/week in patients that did not achieve clinical remission by 8 weeks, as tolerated.
Treatment Compound:Methotrexate
Treatment Route:Subcutaneous or Oral
Treatment Dose:15-20 mg/week
Treatment Doseduration:16 weeks

Sample Preparation:

Sampleprep ID:SP002033
Sampleprep Summary:Plasma samples were sent to the West Coast Metabolomics Center and were processed according to laboratory Standard Operating Procedures for samples preparations of blood plasma or serum samples for lipidomic, biogenic amine, and primary metabolomic analysis using a biphasic MeOH/MTBE/Water extraction procedure. The upper organic phase was used for lipidomics analysis and the aqueous phase was used for analysis of primary metabolism and biogenic amines.
Sampleprep Protocol Filename:Biogenic_Amines.Data Processing
Lipidomics.Data Processing
Primary_Metabolism.Data_Processing

Combined analysis:

Analysis ID AN003173
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus IV
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units Peak Height Intensity

Chromatography:

Chromatography ID:CH002346
Instrument Name:Leco Pegasus IV
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS002951
Analysis ID:AN003173
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:POSITIVE
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