{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001642","ANALYSIS_ID":"AN002687","VERSION":"1","CREATED_ON":"January 11, 2021, 2:41 pm"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"sbhattacharya@med.miami.edu","PHONE":"305-482-4103"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"140365",
"Sample ID":"1",
"Factors":{"Disease status":"HRT1D"},
"Additional sample data":{"RAW_FILE_NAME":"1_pos.raw 1_pos_2.raw 1_neg.raw 1_neg_2.raw"}
},
{
"Subject ID":"2019 0605 TL",
"Sample ID":"2",
"Factors":{"Disease status":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"2_pos.raw 2_pos_2.raw 2_neg.raw 2_neg_2.raw"}
},
{
"Subject ID":"467191",
"Sample ID":"3",
"Factors":{"Disease status":"NOPP"},
"Additional sample data":{"RAW_FILE_NAME":"3_pos.raw 3_pos_2.raw 3_neg.raw 3_neg_2.raw"}
},
{
"Subject ID":"467191 small",
"Sample ID":"4",
"Factors":{"Disease status":"NOF"},
"Additional sample data":{"RAW_FILE_NAME":"4_pos.raw 4_pos_2.raw 4_neg.raw 4_neg_2.raw"}
},
{
"Subject ID":"145569",
"Sample ID":"5",
"Factors":{"Disease status":"HRT1D"},
"Additional sample data":{"RAW_FILE_NAME":"5_pos.raw 5_pos_2.raw 5_neg.raw 5_neg_2.raw"}
},
{
"Subject ID":"2019 0605 BH",
"Sample ID":"6",
"Factors":{"Disease status":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"6_pos.raw 6_pos_2.raw 6_neg.raw 6_neg_2.raw"}
},
{
"Subject ID":"2019 0605 YM",
"Sample ID":"7",
"Factors":{"Disease status":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"7_pos.raw 7_pos_2.raw 7_neg.raw 7_neg_2.raw"}
},
{
"Subject ID":"245361",
"Sample ID":"8",
"Factors":{"Disease status":"HRT1D"},
"Additional sample data":{"RAW_FILE_NAME":"8_pos.raw 8_pos_2.raw 8_neg.raw 8_neg_2.raw"}
},
{
"Subject ID":"2019 0605 MG",
"Sample ID":"9",
"Factors":{"Disease status":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"9_pos.raw 9_pos_2.raw 9_neg.raw 9_neg_2.raw"}
}
],
"COLLECTION":{"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_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)."},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Accela 600","COLUMN_NAME":"Thermo Acclaim 120 (150 x 2.1mm, 3um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Xcalibur software. LipidSearch for data processing."},

"MS_METABOLITE_DATA":{
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