Summary of study ST001690

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 PR001086. The data can be accessed directly via it's Project DOI: 10.21228/M8B123 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 IDST001690
Study TitleUntargeted metabolomic analysis of human blood samples via qualitative GC-MS for T1D biomarker identification
Study TypeQualitative GC-MS biomarker identification
Study Summary"Blood from human subjects at high risk for T1D (and healthy controls; n=4 each) were subjected to parallel unlabeled proteomics, metabolomics, lipidomics, and transcriptomics. The integrated dataset was analyzed using Ingenuity Pathway Analysis (IPA) software for disturbances in the at-risk subjects compared to the controls. The final quadra-omics dataset contained 2292 proteins, 328 miRNAs, 75 metabolites, and 41 lipids that were detected in all samples. Disease/function enrichment analyses consistently indicated increased activation, proliferation, and migration of immune cells, particularly, CD4 T-lymphocytes and macrophages. Integrated molecular network predictions highlighted central involvement and activation of NF-κB, TGF-β, VEGF, arachidonic acid, and arginase, and inhibition of miRNA Let-7a-5p. Parallel multi-omics provided a comprehensive picture of disturbances in high-risk T1D subjects and helped identify an associated integrated biomarker signature, which could ultimately facilitate the classification of T1D progressors from non-progressors."
Institute
Duke University
DepartmentDuke Molecular Physiology Institute, School of Medicine
LaboratoryMetabolomics
Last NameBain
First NameJames
Address300 N Duke St, Durham, NC, 27701, USA
Emailjames.bain@duke.edu
Phone919 479 2320
Submit Date2021-02-09
Total Subjects9
Raw Data AvailableYes
Analysis Type DetailGC-MS
Release Date2021-06-10
Release Version1
James Bain James Bain
https://dx.doi.org/10.21228/M8B123
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001086
Project DOI:doi: 10.21228/M8B123
Project Title:Parallel multi-omics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes
Project Type:Untargeted metabolomics: MS qualitative analysis
Project Summary:MS qualitative analysis of human blood samples to identify early-identification biomarkers for type 1 diabetes
Institute:Duke University
Department:Duke Molecular Physiology Institute, School of Medicine
Laboratory:Metabolomics
Last Name:Bain
First Name:James
Address:300 N Duke Street, Durham, NC, 27701, USA
Email:james.bain@duke.edu
Phone:919 479 2320
Funding Source:NIH, NIDDK
Project Comments:This data represents the untargeted metabolomic analysis of the samples
Contributors:O. Alcazar, L.F. Hernandez, E.S. Nakayasu, C. Ansong, C.D. Nicora, C. Ansong, M.J. Muehlbauer, J.R. Bain, C.J. Myer, S.J. Bhattacharya, P. Buchwald, and M.H. Abdulreda

Subject:

Subject ID:SU001767
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Condition
SA156644RT-
SA1566459Healthy control
SA1566467Healthy control
SA1566476Healthy control
SA1566482Healthy control
SA1566491High-risk T1D
SA1566505High-risk T1D
SA1566518High-risk T1D
SA1566524New-onset (fasting)
SA1566533New-onset (post-prandial)
SA156654Ghost (blank)Process blank
Showing results 1 to 11 of 11

Collection:

Collection ID:CO001760
Collection Summary:"Blood samples (~20 mL/subject in EDTA) were collected from consented male/female subjects considered at high risk for T1D during routine visits as part of the ongoing TrialNet’s Natural History Study of the Development of Type 1 Diabetes (Pathway to Prevention Study) TN-01 study (n=4)."
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001780
Treatment Summary:"Subjects in the TN-01 study are tested semi-annually for the appearance of new or additional autoantibodies and are evaluated metabolically by oral glucose tolerance test (OGTT) to assess their progression toward clinical diagnosis of T1D. Samples from healthy subjects (n=4) were collected as part of another study approved by the IRB of the University of Miami (study number 11995-115). These trials are conducted in accordance with the principles of the Declaration of Helsinki and consistent with the Good Clinical Practice guidelines of the International Conference on Harmonization. The protocol for the ancillary study, under which the current multi-omics analyses were performed, was approved by TrialNet (study ID number 195) and its IRB. The four high-risk subjects in the present report were staged for their risk level according to the TrialNet staging/scoring system, which considers family history, genetic susceptibility according to haplotype (e.g., HLA-DQ/DR), the number of autoantibodies, and OGTT results as follows: low-risk (1 autoantibody and normal OGTT); moderate-risk (2–3 autoantibodies and normal OGTT); high-risk (4–5 autoantibodies and normal OGTT); and very high-risk (4–5 autoantibodies and abnormal OGTT)."

Sample Preparation:

Sampleprep ID:SP001773
Sampleprep Summary:See uploaded protocol
Sampleprep Protocol Filename:Toadpup1956_20210209_120248_PR_SP_PlasmaPrep_non-targeted_MBX.pdf
Sampleprep Protocol Comments:Please treat these as confidential disclosures of in-house sample prep.

Combined analysis:

Analysis ID AN002760
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975B
Ion Mode POSITIVE
Units minutes

Chromatography:

Chromatography ID:CH002040
Methods Filename:Toadpup1956_20210209_120248_PR_MS_Data_acquisition_protocol.pdf
Instrument Name:Agilent 6890N
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002557
Analysis ID:AN002760
Instrument Name:Agilent 5975B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:Acquired using Agilent MassHunter Acquisition software. Feature assignment completed using AMDIS Analysis.
Ion Mode:POSITIVE
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