Summary of Study ST001642

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 PR001050. The data can be accessed directly via it's Project DOI: 10.21228/M8ZX18 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001642
Study TitleLipidomics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes
Study SummaryWe present the lipidome of plasma collected from high-risk type 1 diabetes subjects. The methyl tert-butyl ether (MTBE) method was used for lipid extraction, followed by high performance liquid chromatography (HPLC) tandem mass spectrometry (LC-MS/MS) using a Q Exactive Orbitrap mass spectrometer and an Accela 600 HPLC. Lipid species were identified and quantified by analyzing the raw files in LipidSearch 4.2. Further analysis was conducted using Graphpad Prism and Ingenuity Pathway Analysis (IPA).
Institute
University of Miami
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone305-482-4103
Submit Date2021-01-06
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-01-25
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M8ZX18
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001050
Project DOI:doi: 10.21228/M8ZX18
Project Title:Parallel multi-omics in high-risk subjects for the identification of integrated biomarker signatures of 4 type 1 diabetes
Project Summary:Biomarkers are of paramount importance for early disease detection and are particularly valuable in type 1 diabetes (T1D) to prevent significant β cell loss before the onset of clinical symptoms. Thus far, single-omics studies have failed to identify such T1D biomarkers. Here, we present proof-of-concept studies to demonstrate the potential for identifying integrated biomarker signature(s) of T1D using parallel multi-omics. 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.
Institute:University of Miami
Last Name:Bhattacharya
First Name:Sanjoy
Address:1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Email:sbhattacharya@med.miami.edu
Phone:305-482-4103

Subject:

Subject ID:SU001719
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 Disease status
SA1512676Control
SA1512682Control
SA1512699Control
SA1512707Control
SA1512718HRT1D
SA1512725HRT1D
SA1512731HRT1D
SA1512744NOF
SA1512753NOPP
Showing results 1 to 9 of 9

Collection:

Collection ID:CO001712
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). 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). During sample collection, one of the four high-risk subjects exhibited signs of abnormal OGTT and was confirmed to have converted to a new-onset patient during a second OGTT and another sample collection two weeks later. Both samples were independently analyzed by multi-omics, and the averaged values for each identified feature in both samples were included in the integrative analyses as part of the high-risk group to avoid further reduction in the subject number. Samples from all subjects were divided into four equal aliquots that were individually subjected to proteomics, metabolomics, lipidomics, and transcriptomics (miRNAs) analyses (i.e., parallel quadra-omics) that were performed in collaboration with the Miami Integrative Metabolomics Research Center (lipidomics), Pacific Northwest National Laboratories (proteomics) [58], Ocean Ridge Biosciences (transcriptomics), and the Stedman Metabolomics Laboratory at Duke University Medical Center (metabolomics).
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001732
Treatment Summary:Plasma was collected from high-risk type 2 diabetes subjects and healthy controls. The methyl tert-butyl ether (MTBE) method was used for lipid extraction, followed by mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS).

Sample Preparation:

Sampleprep ID:SP001725
Sampleprep Summary:Lipids were extracted from 50 µL of plasma by adding 4 mL of methyl tert-butyl ether (MTBE) and 1.2 mL of butylated hydroxytoluene (BHT) then incubating overnight at 4°C. The following day, 1.25 mL of 0.15 M ammonium acetate was added, and the samples were centrifuged at 2,000 x g for 10 minutes at 4°C to obtain phase separation. The upper organic phase was collected and the extracted lipids equivalent to 100 µg of protein were dried in a speed vacuum concentrator. The samples were reconstituted in 50 µL of chloroform:methanol (1:1) and sonicated before analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The lipids were analyzed by LC-MS/MS using an Accela 600 HPLC and a Q Exactive Orbitrap mass spectrometer.

Combined analysis:

Analysis ID AN002687
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Accela 600
Column Thermo Acclaim 120 (150 x 2.1mm,3um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001981
Instrument Name:Thermo Accela 600
Column Name:Thermo Acclaim 120 (150 x 2.1mm,3um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002486
Analysis ID:AN002687
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Xcalibur software. LipidSearch for data processing.
Ion Mode:POSITIVE
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