Summary of Study ST000020

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 PR000019. The data can be accessed directly via it's Project DOI: 10.21228/M8TG6F This work is supported by NIH grant, U2C- DK119886.

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Study IDST000020
Study TitleBiomarker Discovery in Knee Osteoarthritis (I)
Study TypeBiomarker Discovery in Knee Osteoarthritis
Study SummaryThe goal of the study was to determine whether there is a set of metabolites that differentiate people who have knee OA and show radiographic disease progression over 18 months from those who have knee OA and do not show disease progression over the same time period.
Institute
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2014-02-28
Num Groups4
Total Subjects88
Raw Data AvailableYes
Raw Data File Type(s)fid
Uploaded File Size53 M
Analysis Type DetailNMR
Release Date2018-08-27
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8TG6F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000019
Project DOI:doi: 10.21228/M8TG6F
Project Title:Intensive Diet and Exercise for Arthritis (IDEA) trial
Project Type:Effects of a calorie-restricting diet, exercise, and a combination of both in reducing knee inflammation and compressive forces in obese and overweight adults with knee osteoarthritis (OA).
Project Summary:Osteoarthritis (OA) is the most common form of arthritis and the number one cause of chronic disability in adults. Interventions which can stop or even slow the progression of OA are badly needed. The long-term goal of this proposal is to use a metabolomics approach to gain a better understanding of metabolic alterations in people with knee osteoarthritis (OA) and to discover novel biomarkers of disease activity. OA results from progressive destruction of the articular cartilage accompanied by hypertrophic changes in adjacent bone, varying degrees of synovial inflammation, and destruction of other joint tissues, including the menisci and ligaments. There are multiple risk factors for OA, including age and joint injury, but perhaps most relevant to this proposal is the role of obesity. The mechanism by which altered metabolism in certain obese individuals might contribute to OA pathogenesis is poorly understood and will be a subject of this proposal. A second critical need in the OA field, which will be addressed by this study, is the availability of biomarkers to detect early disease, predict which people are more likely to progress, or measure response to therapy. Our general hypothesis for this pilot study is that metabolic differences, measured by a metabolomic analysis of urine samples, can be used to distinguish overweight and obese individuals who develop symptomatic knee OA from those who do not and distinguish those with OA who will progress. To test this hypothesis our specific aims are to: 1) Determine if metabolic differences, detected by a comprehensive metabolomics analysis, can be used to distinguish people who will develop symptomatic knee OA from those who will not and 2) Determine if metabolic differences, detected by a comprehensive metabolomics analysis, distinguish people with knee OA who exhibit radiographic progression during an 18 month exercise and weight loss intervention from those who do not.
Institute:Wake Forest University
Department:Molecular Medicine, School of Medicine
Laboratory:Loeser Laboratory
Last Name:Loeser
First Name:Richard
Address:Medical Center Blvd, Winsten-Salem, NC
Email:rloeser@wakehealth.edu
Phone:(336) 716-4322
Funding Source:NIH

Subject:

Subject ID:SU000037
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:56-78
Weight Or Weight Range:Obese or Overweight
Gender:Male, Female
Human Race:Caucasian, African American
Human Trial Type:Intervention
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Time Point Progressor Intervention Race Gender
SA0012451338-fu18fu18 N Diet&Exer B M
SA0012463727-fu18fu18 N Diet&Exer W F
SA0012473166-fu18fu18 N Diet&Exer W F
SA0012481380-fu18fu18 N Diet&Exer W F
SA0012492370-fu18fu18 N Diet&Exer W F
SA0012503163-fu18fu18 N Diet&Exer W F
SA0012512925-fu18fu18 N Diet&Exer W F
SA0012522120-fu18fu18 N Diet&Exer W M
SA0012531538-fu18fu18 N Diet&Exer W M
SA0012543994-fu18fu18 N Diet&Exer W M
SA0012551401-fu18fu18 N Diet&Exer W M
SA0012364272-fu18fu18 N Diet Only B F
SA0012371882-fu18fu18 N Diet Only B M
SA0012383130-fu18fu18 N Diet Only W F
SA0012393296-fu18fu18 N Diet Only W F
SA0012401864-fu18fu18 N Diet Only W F
SA0012412479-fu18fu18 N Diet Only W F
SA0012421382-fu18fu18 N Diet Only W F
SA0012431702-fu18fu18 N Diet Only W F
SA0012443285-fu18fu18 N Diet Only W M
SA0012562944-fu18fu18 N Exer Only W F
SA0012573786-fu18fu18 N Exer Only W F
SA0012653612-fu18fu18 P Diet&Exer B F
SA0012662095-fu18fu18 P Diet&Exer W F
SA0012673985-fu18fu18 P Diet&Exer W F
SA0012682012-fu18fu18 P Diet&Exer W F
SA0012691934-fu18fu18 P Diet&Exer W F
SA0012701808-fu18fu18 P Diet&Exer W M
SA0012711441-fu18fu18 P Diet&Exer W M
SA0012721681-fu18fu18 P Diet&Exer W M
SA0012731291-fu18fu18 P Diet&Exer W M
SA0012582830-fu18fu18 P Diet Only B F
SA0012593929-fu18fu18 P Diet Only W F
SA0012603331-fu18fu18 P Diet Only W F
SA0012613706-fu18fu18 P Diet Only W F
SA0012623750-fu18fu18 P Diet Only W F
SA0012632276-fu18fu18 P Diet Only W F
SA0012642924-fu18fu18 P Diet Only W F
SA0012741745-fu18fu18 P Exer Only B F
SA0012751488-fu18fu18 P Exer Only B M
SA0012764097-fu18fu18 P Exer Only W F
SA0012771106-fu18fu18 P Exer Only W F
SA0012783845-fu18fu18 P Exer Only W M
SA0012791624-fu18fu18 P Exer Only W M
SA0012011338-RVRV N Diet&Exer B M
SA0012021380-RVRV N Diet&Exer W F
SA0012032925-RVRV N Diet&Exer W F
SA0012043166-RVRV N Diet&Exer W F
SA0012053727-RVRV N Diet&Exer W F
SA0012063163-RVRV N Diet&Exer W F
SA0012072370-RVRV N Diet&Exer W F
SA0012082120-RVRV N Diet&Exer W M
SA0012093994-RVRV N Diet&Exer W M
SA0012101401-RVRV N Diet&Exer W M
SA0012111538-RVRV N Diet&Exer W M
SA0011924272-RVRV N Diet Only B F
SA0011931882-RVRV N Diet Only B M
SA0011941864-RVRV N Diet Only W F
SA0011953130-RVRV N Diet Only W F
SA0011961702-RVRV N Diet Only W F
SA0011973296-RVRV N Diet Only W F
SA0011982479-RVRV N Diet Only W F
SA0011991382-RVRV N Diet Only W F
SA0012003285-RVRV N Diet Only W M
SA0012123786-RVRV N Exer Only W F
SA0012132944-RVRV N Exer Only W F
SA0012213612-RVRV P Diet&Exer B F
SA0012222095-RVRV P Diet&Exer W F
SA0012233985-RVRV P Diet&Exer W F
SA0012241934-RVRV P Diet&Exer W F
SA0012252012-RVRV P Diet&Exer W F
SA0012261291-RVRV P Diet&Exer W M
SA0012271808-RVRV P Diet&Exer W M
SA0012281681-RVRV P Diet&Exer W M
SA0012291441-RVRV P Diet&Exer W M
SA0012142830-RVRV P Diet Only B F
SA0012153331-RVRV P Diet Only W F
SA0012163706-RVRV P Diet Only W F
SA0012173750-RVRV P Diet Only W F
SA0012183929-RVRV P Diet Only W F
SA0012192924-RVRV P Diet Only W F
SA0012202276-RVRV P Diet Only W F
SA0012301745-RVRV P Exer Only B F
SA0012311488-RVRV P Exer Only B M
SA0012321106-RVRV P Exer Only W F
SA0012334097-RVRV P Exer Only W F
SA0012343845-RVRV P Exer Only W M
SA0012351624-RVRV P Exer Only W M
Showing results 1 to 88 of 88

Collection:

Collection ID:CO000020
Collection Summary:Urine samples (early morning [second morning void) after a 10-hour fast]) collected from 44 overweight or obese participants in the IDEA trial at baseline and at 18 months of follow-up were selected from two subgroups (n=22 each): a group that exhibited radiographic progression and an age, race, sex, and BMI matched group who did not progress. Progression was defined radiographically by a ≥ 0.7mm decrease in medial JSW from baseline to 18 months while non-progression was defined as a decrease in medial JSW of ≤0.35mm . All subjects experienced knee pain and had radiographic evidence of tibiofemoral OA. For those people who were assigned an intervention that included exercise, the 18-month samples were collected at least 24 hours after the last acute bout of exercise training. In addition sampling was postponed (1-2 weeks after recovery from symptoms) in the event of an acute respiratory, urinary tract, or other infection. Urine was aliquoted and stored in cryovials at -80°C.
Sample Type:Urine
Collection Frequency:Baseline and after 18 month (Follow up)
Volumeoramount Collected:1.8 mL of urine
Storage Conditions:80C.

Treatment:

Treatment ID:TR000038

Sample Preparation:

Sampleprep ID:SP000033
Sampleprep Summary:Chenomx Internal Standard solution (70 ul) and 230 ul D20 was added to each of the 88 urine sample (400 ul), vortexed for 30s, and centrifuged at 12000 rcf for 5min. Chenomx ISTD (Chenomx, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) in D2O. 600 µl aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany). Phenotypic pooled urine samples were made by combining 200 µl aliquots from each of the study samples belonging to the same phenotype (Progressors-Baseline, Progressors-follow up, Non-progressors-baseline, and Non-progressors-follow up). In addition, a combined phenotypic pooled sample was also prepared by using 500 µl aliquot from each of the phenotypic pooled sample. Pooled NMR samples were prepared as described above and used as quality check (QC) samples.
Sampleprep Protocol ID:RTI NMR SERUM CHENOMX method
Sampleprep Protocol Filename:RTI_WOA_IDEA_Metabolomics_Procedure_Feb28_2014.docx
Processing Method:Dilution using a mixture of D2O and Chenomx ISTD
Processing Storage Conditions:On ice
Extraction Method:None

Analysis:

Analysis ID:AN000039
Laboratory Name:RTI/DHMRI
Analysis Type:NMR
Acquisition Date:2013-07-17
Software Version:Topspin/ 3.0
Operator Name:Wimal Pathmasiri, Kevin Knagge
Randomization Order:Yes
Data Format:fid, 1r
Chromatography ID:CH000021
Num Factors:34
Num Metabolites:24

NMR:

NMR ID:NM000005
Analysis ID:AN000039
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5 mM
Spectrometer Frequency:950 MHz
NMR Probe:cryo, inverse ATMA
NMR Solvent:D2O
NMR Tube Size:5mm x 7 in
Shimming Method:topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:12.15 us
Power Level:12.589w
Receiver Gain:4
Offset Frequency:4469.3 Hz
Chemical Shift Ref Cpd:DSS
Temperature:298 K
Number Of Scans:64
Dummy Scans:4
Acquisition Time:0.865 sec
Relaxation Delay:2 sec
Spectral Width:18939.40 Hz
Num Data Points Acquired:32K
Real Data Points:64K
Line Broadening:0.5
Zero Filling:yes
Apodization:lorentzian
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:DSS
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