Summary of Study ST000800

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 PR000576. The data can be accessed directly via it's Project DOI: 10.21228/M86X1F 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 IDST000800
Study TitleInsights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
Study TypeObservational
Study SummaryThe pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2017-07-19
Study CommentsKey: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
PublicationsInsights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics. Scientific Reports volume 8, Article number: 10056 (2018). Dorottya Nagy-Szakal, Dinesh K. Barupal, Bohyun Lee, Xiaoyu Che, Brent L. Williams, Ellie J. R. Kahn, Joy E. Ukaigwe, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, Jose G. Montoya, Daniel L. Peterson, Bruce Levin, Mady Hornig, Oliver Fiehn & W. Ian Lipkin.
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2018-08-16
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M86X1F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000576
Project DOI:doi: 10.21228/M86X1F
Project Title:Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
Project Summary:The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls.
Institute:Columbia University
Department:Center for Infection and Immunity, Mailman School of Public Health
Last Name:Lipkin
First Name:Ian
Address:722 West 168th Street, Room 1703a, New York, NY USA 10032
Email:wil2001@columbia.edu
Phone:212-342-9044
Publications:Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics. Scientific Reports volume 8, Article number: 10056 (2018). Dorottya Nagy-Szakal, Dinesh K. Barupal, Bohyun Lee, Xiaoyu Che, Brent L. Williams, Ellie J. R. Kahn, Joy E. Ukaigwe, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, Jose G. Montoya, Daniel L. Peterson, Bruce Levin, Mady Hornig, Oliver Fiehn & W. Ian Lipkin.

Subject:

Subject ID:SU000825
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 CaseStatus SEX AGE_DICH
SA043899ESP-0514Case Female 20_50
SA043900ESP-0501Case Female 20_50
SA043901ESP-0332Case Female 20_50
SA043902ESP-0566Case Female 20_50
SA043903ESP-0280Case Female 20_50
SA043904ESP-0345Case Female 20_50
SA043905ESP-0891Case Female 20_50
SA043906ESP-0995Case Female 20_50
SA043907ESP-1047Case Female 20_50
SA043908ESP-0228Case Female 20_50
SA043909ESP-0865Case Female 20_50
SA043910ESP-0683Case Female 20_50
SA043911ESP-0592Case Female 20_50
SA043912ESP-0605Case Female 20_50
SA043913ESP-0189Case Female 20_50
SA043914ESP-0124Case Female 20_50
SA043915ESP-0137Case Female 20_50
SA043916ESP-0761Case Female over50
SA043917ESP-0800Case Female over50
SA043918ESP-0878Case Female over50
SA043919ESP-0709Case Female over50
SA043920ESP-0657Case Female over50
SA043921ESP-0085Case Female over50
SA043922ESP-0046Case Female over50
SA043923ESP-0696Case Female over50
SA043924ESP-0956Case Female over50
SA043925ESP-1138Case Female over50
SA043926ESP-1151Case Female over50
SA043927ESP-1164Case Female over50
SA043928ESP-0007Case Female over50
SA043929ESP-1125Case Female over50
SA043930ESP-0020Case Female over50
SA043931ESP-0488Case Female over50
SA043932ESP-0982Case Female over50
SA043933ESP-1034Case Female over50
SA043934ESP-0943Case Female over50
SA043935ESP-0748Case Female over50
SA043936ESP-0423Case Female over50
SA043937ESP-0241Case Female over50
SA043938ESP-0306Case Female over50
SA043939ESP-0215Case Female over50
SA043940ESP-1203Case Male 20_50
SA043941ESP-0072Case Male over50
SA043942ESP-0813Case Male over50
SA043943ESP-0033Case Male over50
SA043944ESP-1255Case Male over50
SA043945ESP-0644Case Male over50
SA043946ESP-0826Case Male over50
SA043947ESP-0904Case Male over50
SA043948ESP-0462Case Male over50
SA043949ESP-1021Control Female 20_50
SA043950ESP-0111Control Female 20_50
SA043951ESP-0579Control Female 20_50
SA043952ESP-0059Control Female 20_50
SA043953ESP-0852Control Female 20_50
SA043954ESP-0176Control Female 20_50
SA043955ESP-0254Control Female 20_50
SA043956ESP-1294Control Female 20_50
SA043957ESP-1268Control Female 20_50
SA043958ESP-1190Control Female 20_50
SA043959ESP-0553Control Female 20_50
SA043960ESP-0098Control Female 20_50
SA043961ESP-0319Control Female 20_50
SA043962ESP-0410Control Female 20_50
SA043963ESP-0618Control Female 20_50
SA043964ESP-0202Control Female 20_50
SA043965ESP-0774Control Female 20_50
SA043966ESP-1112Control Female over50
SA043967ESP-0371Control Female over50
SA043968ESP-1099Control Female over50
SA043969ESP-1086Control Female over50
SA043970ESP-0839Control Female over50
SA043971ESP-0267Control Female over50
SA043972ESP-0722Control Female over50
SA043973ESP-0527Control Female over50
SA043974ESP-0449Control Female over50
SA043975ESP-0384Control Female over50
SA043976ESP-1177Control Female over50
SA043977ESP-1060Control Female over50
SA043978ESP-0293Control Female over50
SA043979ESP-0670Control Female over50
SA043980ESP-0930Control Female over50
SA043981ESP-0917Control Female over50
SA043982ESP-0475Control Female over50
SA043983ESP-0358Control Female over50
SA043984ESP-0969Control Female over50
SA043985ESP-1229Control Female over50
SA043986ESP-0397Control Female over50
SA043987ESP-1008Control Female over50
SA043988ESP-0787Control Female over50
SA043989ESP-0436Control Female over50
SA043990ESP-1281Control Male 20_50
SA043991ESP-1307Control Male 20_50
SA043992ESP-1073Control Male 20_50
SA043993ESP-0163Control Male over50
SA043994ESP-0150Control Male over50
SA043995ESP-0631Control Male over50
SA043996ESP-0735Control Male over50
SA043997ESP-0540Control Male over50
SA043998ESP-1216Control Male over50
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Collection:

Collection ID:CO000819
Collection Summary:Subjects included 50 cases and 50 controls from the Chronic Fatigue Initiative (CFI) Cohort (28) recruited at 4 sites across the US who met the 1994 CDC Fukuda and/or Canadian consensus criteria for ME/CFS.
Sample Type:Blood
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000839
Treatment Summary:Subjects included 50 cases and 50 controls from the Chronic Fatigue Initiative (CFI) Cohort (28) recruited at 4 sites across the US who met the 1994 CDC Fukuda and/or Canadian consensus criteria for ME/CFS.

Sample Preparation:

Sampleprep ID:SP000832
Sampleprep Summary:1.Thaw each 20 μL plasma aliquot at room temperature (see Aliquoting TEDDY samples SOP). Once thawed (~10min) place liquid plasma samples on ice. 2. Add 225 μL cold “MeOH with QC mix” (see SOP “QC mix for LC-MS lipid analysis”). Keep MeOH on ice during extraction 3. Vortex each sample for 10s, keeping the rest on ice during all the extraction. 4. Add 750 μL of cold MTBE with 22:1 CE, keep MTBE on ice during extraction 5. Vortex for 10s 6. Shake for 6min at 4°C in the orbital mixer. 7. Add 188 μL room temperature LC/MS grade water. 8. Vortex for 20 s 9. Centrifuge for 2 min @ 14,000 rcf (12300 rpm) 10. Remove supernatant, splitting into two aliquots of 350 μL, keeping one at –20°C for backup 11. Dry samples to complete dryness in the speed vacuum concentration system
Sampleprep Protocol Filename:SOP_Extraction_of_plasma.pdf

Combined analysis:

Analysis ID AN001271 AN001272
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6530 Agilent 6550
Column Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Counts Counts

Chromatography:

Chromatography ID:CH000887
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Injection Temperature:4 C
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:1.67 uL
Solvent A:60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate
Analytical Time:13 min
Capillary Voltage:3500 eV
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Strong Wash Solvent Name:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:Reversed phase
  
Chromatography ID:CH000888
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6550
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Injection Temperature:4 C
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:5.0 uL
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate
Analytical Time:13 min
Capillary Voltage:3500 eV
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Strong Wash Solvent Name:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:Reversed phase

MS:

MS ID:MS001164
Analysis ID:AN001271
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500 eV
Collision Energy:25 eV
Collision Gas:Nitrogen
Dry Gas Flow:8L/min
Dry Gas Temp:325 C
Fragment Voltage:120 eV
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325 C
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 L/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dyamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS001165
Analysis ID:AN001272
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500 eV
Collision Energy:40 eV
Collision Gas:Nitrogen
Dry Gas Flow:13L/min
Dry Gas Temp:200 C
Fragment Voltage:175 eV
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325 C
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 L/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dyamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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