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.
| Study ID | ST001690 |
| Study Title | Untargeted metabolomic analysis of human blood samples via qualitative GC-MS for T1D biomarker identification |
| Study Type | Qualitative 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 |
| Department | Duke Molecular Physiology Institute, School of Medicine |
| Laboratory | Metabolomics |
| Last Name | Bain |
| First Name | James |
| Address | 300 N Duke St, Durham, NC, 27701, USA |
| james.bain@duke.edu | |
| Phone | 919 479 2320 |
| Submit Date | 2021-02-09 |
| Total Subjects | 9 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-06-10 |
| Release Version | 1 |
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 |
|---|---|---|
| SA156644 | RT | - |
| SA156645 | 9 | Healthy control |
| SA156646 | 7 | Healthy control |
| SA156647 | 6 | Healthy control |
| SA156648 | 2 | Healthy control |
| SA156649 | 1 | High-risk T1D |
| SA156650 | 5 | High-risk T1D |
| SA156651 | 8 | High-risk T1D |
| SA156652 | 4 | New-onset (fasting) |
| SA156653 | 3 | New-onset (post-prandial) |
| SA156654 | Ghost (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 |
| Analysis Protocol File: | Toadpup1956_20210209_120248_PR_MS_Data_acquisition_protocol.pdf |
