Summary of Study ST001908

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 PR001202. The data can be accessed directly via it's Project DOI: 10.21228/M8BD7S This work is supported by NIH grant, U2C- DK119886.

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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 IDST001908
Study TitlePost Acute Myocardial Infarction Left Ventricular Remodeling Bio marker Analysis (PAMILA)
Study SummaryPatients with acute myocardial infarction (a condition classified under coronary heart disease, including STEMI and NSTEMI) are at high risk for recurrent ischemic events, but the pathways and factors which contribute to this elevated risk are incompletely understood. This study aims to identify biomarkers associated with acute myocardial infarction through various omics strategies. For the identified biomarkers, we aim to demonstrate prognostic value, and predict/stratify the risks of adverse cardiovascular events (e.g., stroke, heart failure, death).
Institute
National University of Singapore
Last NameLim
First NameSi Ying
AddressDepartment of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
Emaillim.siying@u.nus.edu
Phone+6592748281
Submit Date2021-08-15
Num Groups2
Total Subjects100
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2022-01-21
Release Version1
Si Ying Lim Si Ying Lim
https://dx.doi.org/10.21228/M8BD7S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001202
Project DOI:doi: 10.21228/M8BD7S
Project Title:Simultaneous metabolite and glycan extraction workflow for joint-omics analysis: a synergistic approach for novel insights into diseases
Project Summary:To synergistically process omics data in an integrative manner, analyte extractions for each omics type need to be done on the same set of clinical samples. Therefore, we introduce a simultaneous dual extraction method for generating both metabolomic and glycomic profiles from one sample with good extraction efficiency and reproducibility. As proof of the usefulness of the extraction and joint-omics workflow, we applied it on platelet samples obtained from a cohort study comprising 66 coronary heart disease (CHD) patients and 34 matched healthy community-dwelling controls. The metabolomics and glycomics datasets were subjected to block partial least square – discriminant analysis (block-PLS-DA) with canonical correlation analysis (CCA) for identifying relevant mechanistic interactions between metabolites and glycans. This joint-omics investigation revealed inter-modulative roles that carbohydrates and amino acids have in metabolic pathways and through intermediate protein dysregulations. It also suggested a protective role of the glyco-redox network in CHD, demonstrating proof-of-principle for a joint-omics analysis in providing new insights into disease mechanisms, as enabled by a simultaneous metabolite-glycan extraction workflow.
Institute:National University of Singapore
Last Name:Lim
First Name:Si Ying
Address:Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
Email:lim.siying@u.nus.edu
Phone:+6592748281

Subject:

Subject ID:SU001986
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Human Inclusion Criteria:a. Clinically diagnosed ST-elevation myocardial infarction (STEMI) • Typical history of ischemic chest pain or angina equivalent symptoms (acute onset dyspnea) • ECG changes of at least 2 contiguous leads of ≥2 mm (0.2 mV) in men or ≥1.5 mm (0.15 mV) in women in leads V2–V3 and/or of ≥1 mm (0.1 mV) in other contiguous chest leads or the limb leads • Presence of Q waves • Typical rise and fall of cardiac enzymes (cTn value exceeding the 99th percentile URL (in ng/L or pg/mL) OR Clinically diagnosed nonST-elevation myocardial infarction (NSTEMI) • ECG changes of ST-segment depression or prominent T-wave inversion and/or • positive biomarkers of necrosis (troponin, CKMB) b. Angiographic findings of >50% occlusion of one or more coronary arteries c. Age>21 years and <85 years, d. Ability to provide written informed consent and comply with study protocol requirements.
Human Exclusion Criteria:a. Patients not able or willing to consent for study b. Severe renal impairment (eGFR<15 ml/min/m2) c. Severe liver impairment d. Anaemia < 8 g/dl (men) and 7 g/dl (women) e. Cardiogenic shock unable to be weaned off inotropes or IABP f. History of significant valvular heart disease (moderate or severe MS, MR, AS, AR, TR) g. History of malignancy diagnosed within the last 12 months h. Patients who cannot be followed up (non-residents)

Factors:

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

mb_sample_id local_sample_id Condition Race Gender Smoker
SA176774P363AMI Chinese Female Current-smoker
SA176775T010AMI Chinese Female Current-smoker
SA176776N319AMI Chinese Female Current-smoker
SA176777N093AMI Chinese Female Non-smoker
SA176778N116AMI Chinese Male Current-smoker
SA176779N124AMI Chinese Male Current-smoker
SA176780N077AMI Chinese Male Current-smoker
SA176781N060AMI Chinese Male Current-smoker
SA176782N308AMI Chinese Male Current-smoker
SA176783N312AMI Chinese Male Current-smoker
SA176784P355AMI Chinese Male Current-smoker
SA176785T067AMI Chinese Male Current-smoker
SA176786P335AMI Chinese Male Current-smoker
SA176787N011AMI Chinese Male Current-smoker
SA176788N315AMI Chinese Male Current-smoker
SA176789T017AMI Chinese Male Current-smoker
SA176790N090AMI Chinese Male Current-smoker
SA176791N128AMI Chinese Male Former-smoker
SA176792P340AMI Chinese Male Former-smoker
SA176793N118AMI Chinese Male Former-smoker
SA176794N059AMI Chinese Male Former-smoker
SA176795N068AMI Chinese Male Former-smoker
SA176796N304AMI Chinese Male Former-smoker
SA176797T041AMI Chinese Male Former-smoker
SA176798N107AMI Chinese Male Non-smoker
SA176799N305AMI Chinese Male Non-smoker
SA176800N316AMI Chinese Male Non-smoker
SA176801N302AMI Chinese Male Non-smoker
SA176802N052AMI Chinese Male Non-smoker
SA176803N310AMI Chinese Male Non-smoker
SA176804N058AMI Chinese Male Non-smoker
SA176805N081AMI Chinese Male Non-smoker
SA176806N008AMI Chinese Male Non-smoker
SA176807N009AMI Chinese Male Non-smoker
SA176808T023AMI Chinese Male Non-smoker
SA176809T034AMI Chinese Male Non-smoker
SA176810N131AMI Chinese Male Non-smoker
SA176811T013AMI Chinese Male Non-smoker
SA176812T044AMI Indian Male Current-smoker
SA176813N074AMI Indian Male Current-smoker
SA176814T036AMI Indian Male Current-smoker
SA176815N108AMI Indian Male Current-smoker
SA176816T033AMI Indian Male Current-smoker
SA176817N092AMI Indian Male Former-smoker
SA176818N082AMI Indian Male Non-smoker
SA176819N064AMI Indian Male Non-smoker
SA176820P338AMI Indian Male Non-smoker
SA176821P353AMI Indian Male Non-smoker
SA176822N122AMI Indian Male Non-smoker
SA176823T043AMI Malay Male Current-smoker
SA176824N112AMI Malay Male Former-smoker
SA176825P341AMI Malay Male Former-smoker
SA176826N130AMI Malay Male Non-smoker
SA176827P334AMI Malay Male Non-smoker
SA176828P369AMI Malay Male Non-smoker
SA176829T030AMI Malay Male Non-smoker
SA176830P364AMI Malay Male Non-smoker
SA176831P339AMI Malay Male Non-smoker
SA176832P332AMI Malay Male Non-smoker
SA176833P337AMI Malay Male Non-smoker
SA176834N317AMI Malay Male Non-smoker
SA176835N119AMI Malay Male Non-smoker
SA176836N057AMI Malay Male Non-smoker
SA176837N078AMI Malay Male Non-smoker
SA176838N102AMI Malay Male Non-smoker
SA176839N026AMI Malay Male Non-smoker
SA176840C007Control Chinese Female Current-smoker
SA176841C034Control Chinese Female Current-smoker
SA176842C011Control Chinese Female Current-smoker
SA176843C014Control Chinese Female Current-smoker
SA176844C074Control Chinese Female Current-smoker
SA176845C076Control Chinese Female Current-smoker
SA176846C078Control Chinese Female Current-smoker
SA176847C021Control Chinese Female Current-smoker
SA176848C061Control Chinese Female Current-smoker
SA176849C060Control Chinese Female Current-smoker
SA176850C048Control Chinese Female Current-smoker
SA176851C052Control Chinese Female Current-smoker
SA176852C040Control Chinese Female Current-smoker
SA176853C006Control Chinese Female Current-smoker
SA176854C053Control Chinese Female Current-smoker
SA176855C038Control Chinese Female Current-smoker
SA176856C049Control Chinese Male Current-smoker
SA176857C080Control Chinese Male Current-smoker
SA176858C073Control Chinese Male Current-smoker
SA176859C070Control Chinese Male Current-smoker
SA176860C050Control Chinese Male Current-smoker
SA176861C047Control Chinese Male Current-smoker
SA176862C030Control Chinese Male Current-smoker
SA176863C071Control Chinese Male Current-smoker
SA176864C012Control Chinese Male Non-smoker
SA176865I014Control Indian Female Current-smoker
SA176866I011Control Indian Female Current-smoker
SA176867I006Control Indian Female Current-smoker
SA176868I025Control Indian Male Current-smoker
SA176869I022Control Indian Male Former-smoker
SA176870M003Control Malay Female Current-smoker
SA176871M005Control Malay Female Current-smoker
SA176872M002Control Malay Male Current-smoker
SA176873M001Control Malay Male Current-smoker
Showing results 1 to 100 of 100

Collection:

Collection ID:CO001979
Collection Summary:1. Collect blood into 2.7 ml citrated vacutainers. 2. Add Theophylline, adenosine and dipyridamole (TAD) solution into the citrated blood to final concentrations of 1.5mM, 0.37mM and 0.0198mM respectively. Mix gently by inverting for 4-6 times. 3. Centrifuge at 150g for 10min, RT 4. Collect PRP (leaving approx. 5mm) into a 5 ml polypropylene tube 5. Centrifuge again at 150g for 10min, RT 6. Collect PRP (leaving approx. 5mm) into the same tube from step 4 7. Add apyrase (final concentration: 0.04 U/mL) and 1 vol of 2.5X TAD-PBS 8. Mix gently by inverting tubes 5 times 9. Centrifuge diluted PRP at 100g for 10 min at RT 10. Transfer supernatant into a new 5 ml polypropylene tube 11. Centrifuge supernatant at 1000g for 10 min 12. Discard supernatant 13. Add 1.5mL of 2.5X TAD/PWD (1.5mM theophylline, 0.37mM adenosine and 0.0198mM dipyridamole in 140mM NaCl, 10mM NaHCO3, 2.5mM KCl, 0.5mM Na2HPO4, 1mM MgCl2, 6.46mM Na3C6H5O7 and 0.1% glucose, pH 6.5) containing apyrase (0.04 U/mL). 14. Gently resuspend and centrifuge at 1000g for 9 min using the tabletop Eppendorf centrifuge 15. Discard supernatant 16. Either keep the platelet pellet -80oC until analysis or resuspended in tyrode’s (134 mM NaCl, 12 mM NaHCO3, 2.9 mM KCl, 0.34 mM Na2HPO4, 1.0 mM MgCl2, 10 mM HEPES and 5 mM glucose, pH 7.4) buffers for flow cytometry analysis.
Sample Type:Platelets
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001998
Treatment Summary:No treatment/intervention was done to the patients prior to sample collection for this project. Platelet samples were obtained from healthy volunteers and patients with coronary heart disease. Medication was given after diagnosis, but they are not included as variables in this project.

Sample Preparation:

Sampleprep ID:SP001992
Sampleprep Summary:Simultaneous extraction of metabolites and glycans.

Combined analysis:

Analysis ID AN003105
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000
Column Waters XBridge Amide (100 x 2.1 mm, 3.5 um)
MS Type ESI
MS instrument type new
MS instrument name ABI Sciex 5500 QTrap
Ion Mode POSITIVE
Units a.u.

Chromatography:

Chromatography ID:CH002292
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge Amide (100 x 2.1 mm, 3.5 um)
Chromatography Type:HILIC

MS:

MS ID:MS002887
Analysis ID:AN003105
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:new
MS Type:ESI
MS Comments:Both Positive and negative modes were used
Ion Mode:POSITIVE
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