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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001642 |
| Study Title | Lipidomics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes |
| Study Summary | We 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 Name | Bhattacharya |
| First Name | Sanjoy |
| Address | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| sbhattacharya@med.miami.edu | |
| Phone | 305-482-4103 |
| Submit Date | 2021-01-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-01-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA151267 | 6 | Control |
| SA151268 | 2 | Control |
| SA151269 | 9 | Control |
| SA151270 | 7 | Control |
| SA151271 | 8 | HRT1D |
| SA151272 | 5 | HRT1D |
| SA151273 | 1 | HRT1D |
| SA151274 | 4 | NOF |
| SA151275 | 3 | NOPP |
| 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 |
