Summary of Study ST003853
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 PR002410. The data can be accessed directly via it's Project DOI: 10.21228/M8425Q 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 | ST003853 |
| Study Title | Exploring Metabolomic Profiles in Vitamin D Deficient and Obese Individuals |
| Study Type | LC/MS/MS |
| Study Summary | Cardiovascular diseases (CVDs) continue to pose a significant global health challenge, with vitamin D (Vit D) deficiency and obesity emerging as prominent risk factors. Arterial stiffness is recognized as a pivotal predictor and an independent risk element for CVDs. This study explores the metabolomic profiling of blood samples obtained from individuals afflicted with early arterial stiffness along with Vit D deficiency and obesity, compared with a healthy control group with normal Vit D and non-obese individuals. The study comprised nine participants with Vit D deficiency (Vit D level of 20 ng/ml or lower), and obese participants (BMI ≥ 30), along with eleven control participants (with Vit D levels above 20 ng/ml and normal BMI). Eleven metabolites exhibited statistically significant differences in patients with Vit D deficiency and obesity. Of these, eight metabolites demonstrated increased levels (FC > 2, p < 0.05), including Nutriacholic acid, N-Acetylputrescine, Succinylacetone, Adenosine monophosphate, Elaidic acid, Niacinamide, DUMP, and 2-Pyrrolidinone, while three metabolites exhibited decreased expression: PC (18:1(9Z)/18:1(9Z)), Trimethylamine, and Imidazole. The enrichment analysis revealed that top metabolic pathways predicted to be altered in the context of dysfunctional enzymes, encompassing processes such as nicotinamide acid uptake, fatty-acyl-CoA synthase (n-C18:0CoA), and extracellular NADP nucleosidase, among others. The ROC analysis showed that the blood metabolite concentrations can reliably differentiate with acceptable accuracy (AUC >0.8, p<0.05) between individuals at risk of arterial stiffness with Vit D deficiency and obesity from healthy controls showing the highest discriminator effect for DUMP and Niacinamide with AUC > 0.9 and p<0.00005. A combination metabolites model calculated with the linear SVM model achieved the highest performance of AUC=0.996 (95% CI: 0.97-1) and a predictive accuracy of 94.5% with the combination of seven metabolites. Integration of metabolomics and previous transcriptomics data identifies among the Vit D deficient and obese group disturbances in metabolic and regulatory pathways potentially related to vascular health such as inositol phosphate metabolism. The average PWV value relative to the participant's age as previously reported was 19.4 ± 4.7 m/s in the group with both Vit D deficiency and obesity, compared to 14.7 ± 2.1 m/s in the healthy control group (p < 0.05), indicating increased arterial stiffness. |
| Institute | Sharjah Institute for Medical Research |
| Department | Research institute of medical and health science |
| Laboratory | Biomarker Discovery Group |
| Last Name | Facility |
| First Name | Core |
| Address | M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates |
| tims-tof@sharjah.ac.ae | |
| Phone | +971 6 5057656 |
| Submit Date | 2025-04-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, d |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-05-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002410 |
| Project DOI: | doi: 10.21228/M8425Q |
| Project Title: | Exploring Metabolomic Profiles in Vitamin D Deficient and Obese Individuals |
| Project Type: | LC-MS/MS |
| Project Summary: | Cardiovascular diseases (CVDs) continue to pose a significant global health challenge, with vitamin D (Vit D) deficiency and obesity emerging as prominent risk factors. Arterial stiffness is recognized as a pivotal predictor and an independent risk element for CVDs. This study explores the metabolomic profiling of blood samples obtained from individuals afflicted with early arterial stiffness along with Vit D deficiency and obesity, compared with a healthy control group with normal Vit D and non-obese individuals. The study comprised nine participants with Vit D deficiency (Vit D level of 20 ng/ml or lower), and obese participants (BMI ≥ 30), along with eleven control participants (with Vit D levels above 20 ng/ml and normal BMI). Eleven metabolites exhibited statistically significant differences in patients with Vit D deficiency and obesity. Of these, eight metabolites demonstrated increased levels (FC > 2, p < 0.05), including Nutriacholic acid, N-Acetylputrescine, Succinylacetone, Adenosine monophosphate, Elaidic acid, Niacinamide, DUMP, and 2-Pyrrolidinone, while three metabolites exhibited decreased expression: PC (18:1(9Z)/18:1(9Z)), Trimethylamine, and Imidazole. The enrichment analysis revealed that top metabolic pathways predicted to be altered in the context of dysfunctional enzymes, encompassing processes such as nicotinamide acid uptake, fatty-acyl-CoA synthase (n-C18:0CoA), and extracellular NADP nucleosidase, among others. The ROC analysis showed that the blood metabolite concentrations can reliably differentiate with acceptable accuracy (AUC >0.8, p<0.05) between individuals at risk of arterial stiffness with Vit D deficiency and obesity from healthy controls showing the highest discriminator effect for DUMP and Niacinamide with AUC > 0.9 and p<0.00005. A combination metabolites model calculated with the linear SVM model achieved the highest performance of AUC=0.996 (95% CI: 0.97-1) and a predictive accuracy of 94.5% with the combination of seven metabolites. Integration of metabolomics and previous transcriptomics data identifies among the Vit D deficient and obese group disturbances in metabolic and regulatory pathways potentially related to vascular health such as inositol phosphate metabolism. The average PWV value relative to the participant's age as previously reported was 19.4 ± 4.7 m/s in the group with both Vit D deficiency and obesity, compared to 14.7 ± 2.1 m/s in the healthy control group (p < 0.05), indicating increased arterial stiffness. |
| Institute: | Sharjah Institute for Medical Research |
| Department: | Research institute of medical and health science |
| Laboratory: | Biomarker Discovery Group |
| Last Name: | Facility |
| First Name: | Core |
| Address: | M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates |
| Email: | tims-tof@sharjah.ac.ae |
| Phone: | +971 6 5057656 |
Subject:
| Subject ID: | SU003987 |
| 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 | Treatment |
|---|---|---|
| SA421997 | Plasma18-01_67_1_2212 | Control |
| SA421998 | Plasma24-02_73_1_2225 | Control |
| SA421999 | Plasma10-02_59_1_2197 | Control |
| SA422000 | Plasma23-02_72_1_2223 | Control |
| SA422001 | Plasma23-01_72_1_2222 | Control |
| SA422002 | Plasma22-02_71_1_2221 | Control |
| SA422003 | Plasma22-01_71_1_2220 | Control |
| SA422004 | Plasma20-02_69_1_2217 | Control |
| SA422005 | Plasma20-01_69_1_2216 | Control |
| SA422006 | Plasma18-02_67_1_2213 | Control |
| SA422007 | Plasma10-01_59_1_2196 | Control |
| SA422008 | Plasma17-02_66_1_2211 | Control |
| SA422009 | Plasma13-01_62_1_2202 | Control |
| SA422010 | Plasma17-01_66_1_2210 | Control |
| SA422011 | Plasma12-01_61_1_2200 | Control |
| SA422012 | Plasma12-02_61_1_2201 | Control |
| SA422013 | Plasma24-01_73_1_2224 | Control |
| SA422014 | Plasma13-02_62_1_2203 | Control |
| SA422015 | Plasma14-02_63_1_2205 | Control |
| SA422016 | Plasma15-01_64_1_2206 | Control |
| SA422017 | Plasma15-02_64_1_2207 | Control |
| SA422018 | Plasma14-01_63_1_2204 | Control |
| SA422019 | Plasma11-01_60_1_2198 | Vit D. Def.+ Obese |
| SA422020 | Plasma25-02_74_1_2227 | Vit D. Def.+ Obese |
| SA422021 | Plasma25-01_74_1_2226 | Vit D. Def.+ Obese |
| SA422022 | Plasma21-02_70_1_2219 | Vit D. Def.+ Obese |
| SA422023 | Plasma21-01_70_1_2218 | Vit D. Def.+ Obese |
| SA422024 | Plasma16-02_65_1_2209 | Vit D. Def.+ Obese |
| SA422025 | Plasma16-01_65_1_2208 | Vit D. Def.+ Obese |
| SA422026 | Plasma11-02_60_1_2199 | Vit D. Def.+ Obese |
| SA422027 | Plasma06-02_55_1_2189 | Vit D. Def.+ Obese |
| SA422028 | Plasma08-02_57_1_2193 | Vit D. Def.+ Obese |
| SA422029 | Plasma08-01_57_1_2192 | Vit D. Def.+ Obese |
| SA422030 | Plasma06-01_55_1_2188 | Vit D. Def.+ Obese |
| SA422031 | Plasma04-02_53_1_2185 | Vit D. Def.+ Obese |
| SA422032 | Plasma02-02_51_1_2181 | Vit D. Def.+ Obese |
| SA422033 | Plasma02-01_51_1_2180 | Vit D. Def.+ Obese |
| SA422034 | Plasma01-02_50_1_2179 | Vit D. Def.+ Obese |
| SA422035 | Plasma01-01_50_1_2178 | Vit D. Def.+ Obese |
| SA422036 | Plasma04-01_53_1_2184 | Vit D. Def.+ Obese |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO003980 |
| Collection Summary: | The study comprised nine participants with Vit D deficiency (Vit D level of 20 ng/ml or lower), and obese participants (BMI ≥ 30), along with eleven control participants (with Vit D levels above 20 ng/ml and normal BMI). Blood Samples were centrifuged for 5 minutes at 5000 rpm at 4°C then the plasma was taken and frozen at -80°C until further analysis. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003996 |
| Treatment Summary: | No treatment was given. The study comprised nine participants with Vit D deficiency (Vit D level of 20 ng/ml or lower), and obese participants (BMI ≥ 30), along with eleven control participants (with Vit D levels above 20 ng/ml and normal BMI). Blood Samples were centrifuged for 5 minutes at 5000 rpm at 4°C then the plasma was taken and frozen at -80°C until further analysis |
Sample Preparation:
| Sampleprep ID: | SP003993 |
| Sampleprep Summary: | Plasma samples were divided into Eppendorf of 100 μL each, 300 μL of methanol ((≥99.9 %, LCMS CHROMASOLV) was added, followed by vortex and incubation at −20 ◦C for 2 h. Next, the samples were vortexed and then centrifuged at 14,000 rpm for 15 min at 4°C. Then, the supernatant was evaporated using Speed vacuum evaporation at 37 ± 1 °C ◦C (EZ-2 Plus (GeneVac, Ipswich, UK). The extract samples were resuspended with 200uL of 0.1% formic acid in deionized water-LCMS CHROMASOLV from Honeywell (Wunstorfer Strasse, Seelze, Germany) and vortexed for 2 min to be mixed totally. Finally, the samples were filtered using a hydrophilic nylon syringe filter of 0.45 μm pore size and returned to the glass insert within LC glass vials. The quality control (QC) sample was prepared by pooling the same volume (10 μL) of each sample, and all samples were placed in the autosampler at a temperature set at 4℃ and analyzed with UHPLC-QTOF-MS. |
Chromatography:
| Chromatography ID: | CH004802 |
| Chromatography Summary: | The Elute UHPLC and Q-TOF Mass Spectrometer (Bruker, Bremen, Germany) were utilized for metabolite detection. The Elute HPG 1300 pumps, Elute Au-tosampler (Bruker, Bremen, Germany), and Hamilton® Intensity Solo 2 C18 column (100 mm x 2.1 mm, 1.8 μm) were employed using reversed-phase chromatography. Solvents used for separation were 0.1 % FA in LC grade water (solvent A) and 0.1 % FA in ACN (solvent B). The column was kept at 35°C, and each sample was injected twice with an injection volume of 10 µL. Sample elution was performed in 30 min gradient starting with 1% ACN for 2 min and then ramped to 99% ACN within 15 min. After that, 99% ACN was kept for 3 min, and then the re-equilibration to 1% ACN was done for 10 min. The flow rate was 0.25 mL/min for 20 min and then 0.35 mL/min for 8.3 min and then the flow rate set at 0.25 mL/min for 1.7 min. |
| Instrument Name: | Bruker timsTOF |
| Column Name: | Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8um) |
| Column Temperature: | 35°C |
| Flow Gradient: | Sample elution was performed in 30 min gradient starting with 1% B for 2 min and then ramped to 99% B within 15 min. After that, 99% B was kept for 3 min, and then the re-equilibration to 1% B was done for 10 min. |
| Flow Rate: | The flow rate was 0.25 mL/min for 20 min and then 0.35 mL/min for 8.3 min and then the flow rate set at 0.25 mL/min for 1.7 min. |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006331 |
| Analysis Type: | MS |
| Analysis Protocol File: | Vitamin_D_Deficient_and_Obese_Protocol.pdf |
| Chromatography ID: | CH004802 |
| Num Factors: | 2 |
| Num Metabolites: | 111 |
| Rt Units: | Minutes |
| Units: | AU |
