Summary of Study ST000802

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

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Study IDST000802
Study TitleInsights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part III))
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)wiff
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:SU000827
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id CaseStatus SEX AGE_DICH
SA044110ESP-0891Case Female 20_50
SA044111ESP-0189Case Female 20_50
SA044112ESP-0345Case Female 20_50
SA044113ESP-0332Case Female 20_50
SA044114ESP-0228Case Female 20_50
SA044115ESP-0280Case Female 20_50
SA044116ESP-0865Case Female 20_50
SA044117ESP-0683Case Female 20_50
SA044118ESP-0137Case Female 20_50
SA044119ESP-0566Case Female 20_50
SA044120ESP-0514Case Female 20_50
SA044121ESP-0501Case Female 20_50
SA044122ESP-0592Case Female 20_50
SA044123ESP-1047Case Female 20_50
SA044124ESP-0995Case Female 20_50
SA044125ESP-0124Case Female 20_50
SA044126ESP-0605Case Female 20_50
SA044127ESP-0007Case Female over50
SA044128ESP-0709Case Female over50
SA044129ESP-0696Case Female over50
SA044130ESP-0748Case Female over50
SA044131ESP-0878Case Female over50
SA044132ESP-1125Case Female over50
SA044133ESP-1138Case Female over50
SA044134ESP-1151Case Female over50
SA044135ESP-1164Case Female over50
SA044136ESP-1034Case Female over50
SA044137ESP-0982Case Female over50
SA044138ESP-0800Case Female over50
SA044139ESP-0488Case Female over50
SA044140ESP-0943Case Female over50
SA044141ESP-0956Case Female over50
SA044142ESP-0761Case Female over50
SA044143ESP-0657Case Female over50
SA044144ESP-0241Case Female over50
SA044145ESP-0085Case Female over50
SA044146ESP-0046Case Female over50
SA044147ESP-0020Case Female over50
SA044148ESP-0306Case Female over50
SA044149ESP-0215Case Female over50
SA044150ESP-0423Case Female over50
SA044151ESP-1203Case Male 20_50
SA044152ESP-1255Case Male over50
SA044153ESP-0826Case Male over50
SA044154ESP-0813Case Male over50
SA044155ESP-0072Case Male over50
SA044156ESP-0033Case Male over50
SA044157ESP-0644Case Male over50
SA044158ESP-0462Case Male over50
SA044159ESP-0904Case Male over50
SA044160ESP-0098Control Female 20_50
SA044161ESP-0111Control Female 20_50
SA044162ESP-0254Control Female 20_50
SA044163ESP-0176Control Female 20_50
SA044164ESP-0202Control Female 20_50
SA044165ESP-0774Control Female 20_50
SA044166ESP-0852Control Female 20_50
SA044167ESP-0059Control Female 20_50
SA044168ESP-1294Control Female 20_50
SA044169ESP-1021Control Female 20_50
SA044170ESP-0579Control Female 20_50
SA044171ESP-0410Control Female 20_50
SA044172ESP-0553Control Female 20_50
SA044173ESP-1268Control Female 20_50
SA044174ESP-0618Control Female 20_50
SA044175ESP-1190Control Female 20_50
SA044176ESP-0319Control Female 20_50
SA044177ESP-1060Control Female over50
SA044178ESP-0436Control Female over50
SA044179ESP-1177Control Female over50
SA044180ESP-0449Control Female over50
SA044181ESP-1086Control Female over50
SA044182ESP-1112Control Female over50
SA044183ESP-0475Control Female over50
SA044184ESP-1099Control Female over50
SA044185ESP-1229Control Female over50
SA044186ESP-0917Control Female over50
SA044187ESP-0722Control Female over50
SA044188ESP-1008Control Female over50
SA044189ESP-0293Control Female over50
SA044190ESP-0527Control Female over50
SA044191ESP-0358Control Female over50
SA044192ESP-0371Control Female over50
SA044193ESP-0670Control Female over50
SA044194ESP-0267Control Female over50
SA044195ESP-0787Control Female over50
SA044196ESP-0397Control Female over50
SA044197ESP-0969Control Female over50
SA044198ESP-0930Control Female over50
SA044199ESP-0384Control Female over50
SA044200ESP-0839Control Female over50
SA044201ESP-1281Control Male 20_50
SA044202ESP-1073Control Male 20_50
SA044203ESP-1307Control Male 20_50
SA044204ESP-0631Control Male over50
SA044205ESP-0735Control Male over50
SA044206ESP-0150Control Male over50
SA044207ESP-0163Control Male over50
SA044208ESP-0540Control Male over50
SA044209ESP-1216Control Male over50
Showing results 1 to 100 of 100

Collection:

Collection ID:CO000821
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:TR000841
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:SP000834
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:SP_SOP_Extraction_of_plasma.pdf

Combined analysis:

Analysis ID AN001274
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex API 4000 QTrap
Ion Mode NEGATIVE
Units Concentration (nM)

Chromatography:

Chromatography ID:CH000890
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
Column Temperature:60 °C
Flow Gradient:0 min 25% (B), 1 min 40% (B), 1-2.5 min 42% (B), 2.5-4.5 50% (B), 4.5-10.5 65% (B), 10.5-12.5 75% (B), 12.5-14 85% (B), 14-14.5 95% (B), 14.5-15 25% (B), 15-16 25% (B)
Flow Rate:0.25 uL
Sample Injection:5 µL
Solvent A:100% water; 0.1% acetic acid
Solvent B:90% acetonitrile/ 10% isopropanol
Analytical Time:16 min
Washing Buffer:Ethyl Acetate
Weak Wash Solvent Name:20% methanol, 10% isopropanol
Weak Wash Volume:600 µL
Strong Wash Solvent Name:50:50 Acetonitrile:Methanol
Strong Wash Volume:600 µL
Sample Loop Size:17 µL
Randomization Order:Excel generated
Chromatography Type:Reversed phase

MS:

MS ID:MS001167
Analysis ID:AN001274
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
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