Summary of Study ST001266
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 PR000851. The data can be accessed directly via it's Project DOI: 10.21228/M8PH4S 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 | ST001266 |
| Study Title | Metabolomic Profiles of Pancreatic β-Cells and Islets Exposed to Arsenic, part I β-Cells |
| Study Summary | Type-2 diabetes (T2D) is a complex metabolic disorder that affects hundreds of millions of people world-wide and is a growing public health concern. Despite recent advances in T2D research, the etiology of this disease and the mechanisms underlying the metabolic defects remain poorly understood. While obesity is thought to be the main cause for the rising prevalence of T2D, obesity alone cannot explain differences in the trends of T2D among different geographical regions and populations. Growing evidence suggests that environmental exposures to toxic and diabetogenic substances must play important roles. Inorganic arsenic (iAs) is a naturally occurring toxic metalloid. Hundreds of millions of people worldwide are exposed to unsafe levels of iAs in drinking water and food. iAs is a potent carcinogen, but iAs exposure has also been linked to increase risk of T2D. While the link between iAs exposure and T2D is well-established, the mechanisms underlying the diabetogenic effects of iAs exposure remain unclear. Results of our previously published and ongoing studies suggest that pancreatic β-cells are a primary target for iAs and its metabolites and that impaired insulin secretion by β-cells is the mechanism by which iAs exposure leads to diabetes. The proposed project will use metabolomics to identify metabolic pathways in β-cells that are targeted by iAs and its metabolites, monomethyl-As (MAs) and dimethyl-As (DMAs). The metabolomics data combined with results of our ongoing mechanistic studies will provide a comprehensive picture of the metabolic dysfunction leading to the development of diabetes in individuals exposed to iAs and of the molecular mechanisms that underlie this dysfunction. Identifying the affected pathways and mechanisms will ultimately help to improve strategies for prevention and/or treatment of T2D associated with chronic exposure to iAs. |
| Institute | University of North Carolina |
| Last Name | Sumner |
| First Name | Susan |
| Address | 500 Laureate Way, Kannapolis, NC 28081 |
| Susan_sumner@unc.edu | |
| Phone | (919)6224456 |
| Submit Date | 2019-04-15 |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-06-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000851 |
| Project DOI: | doi: 10.21228/M8PH4S |
| Project Title: | Metabolomic Profiles of Pancreatic β-Cells and Islets Exposed to Arsenic |
| Project Summary: | Type-2 diabetes (T2D) is a complex metabolic disorder that affects hundreds of millions of people world-wide and is a growing public health concern. Despite recent advances in T2D research, the etiology of this disease and the mechanisms underlying the metabolic defects remain poorly understood. While obesity is thought to be the main cause for the rising prevalence of T2D, obesity alone cannot explain differences in the trends of T2D among different geographical regions and populations. Growing evidence suggests that environmental exposures to toxic and diabetogenic substances must play important roles. Inorganic arsenic (iAs) is a naturally occurring toxic metalloid. Hundreds of millions of people worldwide are exposed to unsafe levels of iAs in drinking water and food. iAs is a potent carcinogen, but iAs exposure has also been linked to increase risk of T2D. While the link between iAs exposure and T2D is well-established, the mechanisms underlying the diabetogenic effects of iAs exposure remain unclear. Results of our previously published and ongoing studies suggest that pancreatic β-cells are a primary target for iAs and its metabolites and that impaired insulin secretion by β-cells is the mechanism by which iAs exposure leads to diabetes. The proposed project will use metabolomics to identify metabolic pathways in β-cells and pancreatic islets that are targeted by iAs and its metabolites, monomethyl-As (MAs) and dimethyl-As (DMAs). The metabolomics data combined with results of our ongoing mechanistic studies will provide a comprehensive picture of the metabolic dysfunction leading to the development of diabetes in individuals exposed to iAs and of the molecular mechanisms that underlie this dysfunction. Identifying the affected pathways and mechanisms will ultimately help to improve strategies for prevention and/or treatment of T2D associated with chronic exposure to iAs. |
| Institute: | University of North Carolina at Chapel Hill |
| Last Name: | Styblo |
| First Name: | Miroslav |
| Address: | Departmnet of Nutrition, CB# 7461, Chapel Hill, NC 27599-7461 |
| Email: | miroslav_styblo@med.unc.edu |
| Phone: | (919) 966-5721 |
Subject:
| Subject ID: | SU001334 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Cell Strain Details: | INS-1 832/13 cell line |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Cell Type | Treatment |
|---|---|---|---|
| SA092008 | SP_CB_1_1 | Beta cell sample pool | - |
| SA092009 | SP_CB_1_2 | Beta cell sample pool | - |
| SA092010 | SP_CB_2_2 | Beta cell sample pool | - |
| SA092011 | SP_CB_2_1 | Beta cell sample pool | - |
| SA092012 | SP_CB_3_1 | Beta cell sample pool | - |
| SA092013 | SP_CB_3_2 | Beta cell sample pool | - |
| SA092014 | SP_CB_4 | Beta cell sample pool | - |
| SA092025 | CB_16 | INS-1 (beta cells) | dimethylated arsenic |
| SA092026 | CB_40 | INS-1 (beta cells) | dimethylated arsenic |
| SA092027 | CB_36 | INS-1 (beta cells) | dimethylated arsenic |
| SA092028 | CB_37 | INS-1 (beta cells) | dimethylated arsenic |
| SA092029 | CB_38 | INS-1 (beta cells) | dimethylated arsenic |
| SA092030 | CB_17 | INS-1 (beta cells) | dimethylated arsenic |
| SA092031 | CB_18 | INS-1 (beta cells) | dimethylated arsenic |
| SA092032 | CB_20 | INS-1 (beta cells) | dimethylated arsenic |
| SA092033 | CB_39 | INS-1 (beta cells) | dimethylated arsenic |
| SA092034 | CB_19 | INS-1 (beta cells) | dimethylated arsenic |
| SA092035 | CB_7 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092036 | CB_9 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092037 | CB_8 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092038 | CB_6 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092039 | CB_30 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092040 | CB_28 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092041 | CB_26 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092042 | CB_10 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092043 | CB_29 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092044 | CB_27 | INS-1 (beta cells) | inorganic arsenic (sodium arsenite) |
| SA092045 | CB_13 | INS-1 (beta cells) | monomethylated arsenic |
| SA092046 | CB_12 | INS-1 (beta cells) | monomethylated arsenic |
| SA092047 | CB_11 | INS-1 (beta cells) | monomethylated arsenic |
| SA092048 | CB_34 | INS-1 (beta cells) | monomethylated arsenic |
| SA092049 | CB_14 | INS-1 (beta cells) | monomethylated arsenic |
| SA092050 | CB_15 | INS-1 (beta cells) | monomethylated arsenic |
| SA092051 | CB_32 | INS-1 (beta cells) | monomethylated arsenic |
| SA092052 | CB_35 | INS-1 (beta cells) | monomethylated arsenic |
| SA092053 | CB_33 | INS-1 (beta cells) | monomethylated arsenic |
| SA092054 | CB_31 | INS-1 (beta cells) | monomethylated arsenic |
| SA092015 | CB_25 | INS-1 (beta cells) | No treatment |
| SA092016 | CB_3 | INS-1 (beta cells) | No treatment |
| SA092017 | CB_1 | INS-1 (beta cells) | No treatment |
| SA092018 | CB_24 | INS-1 (beta cells) | No treatment |
| SA092019 | CB_4 | INS-1 (beta cells) | No treatment |
| SA092020 | CB_5 | INS-1 (beta cells) | No treatment |
| SA092021 | CB_23 | INS-1 (beta cells) | No treatment |
| SA092022 | CB_21 | INS-1 (beta cells) | No treatment |
| SA092023 | CB_2 | INS-1 (beta cells) | No treatment |
| SA092024 | CB_22 | INS-1 (beta cells) | No treatment |
| Showing results 1 to 47 of 47 |
Collection:
| Collection ID: | CO001328 |
| Collection Summary: | Cells were trypsinized for approximately 30 seconds. Once collected, the cells were centrifuged at 1200 rpm for 5 minutes to form a pellet. The cell pellet was washed using PBS. |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001349 |
| Treatment Summary: | INS-1 832/13 cells were seeded at a density of 1 million cells per well on a 12-well plate, and exposed to 2 µM iAsIII (sodium arsenite, > 99% pure; Sigma-Aldrich, St. Louis, MO), 0.2 µM MAsIII (methylarsine oxide, > 98% pure), or 2 µM DMAsIII (Iododimethylarsine, > 98% Pure; Sigma Aldrich, St. Louis, MO) for 24h prior to glucose stimulated insulin secretion or metabolomics. Cells treated with medium without any kind of As were used as Control. |
| Cell Storage: | -80 °C |
Sample Preparation:
| Sampleprep ID: | SP001342 |
| Sampleprep Summary: | The frozen beta-cell samples were put on dry ice with a randomized order. A volume of 400 µL methanol-water (80:20) was added to the cells and vortexed by a multi-tube vortexer for 5 min at 5000 rpm. All contents in the tube were transferred into a pre-labeled MagNaLyzer tube (with 10-15 beads inside). The tubes were put on the bead homogenizer using quick run setting for bacterial cells (2 ml) with speed at 6.30 m/s for 45 sec in 1 cycle. All samples were centrifuged at 16,000 rcf for 5 min at 4°C. Supernatant from individual sample was transferred into a pre-labeled 1.5 ml low-bind Eppendorf tube. All the samples were centrifuged at 16,000 rcf for 20 min at 4°C. For quality control purpose, 32 µl of the supernatant from individual sample was transferred into a new 2-ml tube to make a sample pool (SP). Aliquots (300 µl) of supernatant from the studied samples and SP were transferred into the pre-labeled 1.5 ml Low-bind Eppendorf tubes. All samples, including studied samples and SPs, were dried using speed-vac. For immediate analysis, 100 µL of Water-Methanol (95:5) was added to the residue, and then thoroughly mixed on multiple tube vortexer for 10 mins at 5000 rpm. After centrifuge at 4°C, 16000 rcf for 4 min, the supernatant from individual sample was transferred to pre-labeled auto-sampler vial for LC-MS analysis. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002103 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | Relative Intensity |
Chromatography:
| Chromatography ID: | CH001535 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| Column Pressure: | 6000-10000 psi |
| Column Temperature: | 50 |
| Flow Rate: | 0.4 ml/min |
| Injection Temperature: | 8 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Analytical Time: | 22 min |
| Capillary Voltage: | 3.75 KV |
| Weak Wash Solvent Name: | 10:90 Methanol:Water with 0.1% FA solution |
| Strong Wash Solvent Name: | 75:25 2-Propanol: Water with 0.1% FA solution |
| Randomization Order: | Yes |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001954 |
| Analysis ID: | AN002103 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | We used DDA mode to acquire the MS and MS/MS data. Progenesis QI was used for peak picking, alignment, and normalization. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 °C |
| Capillary Voltage: | 3.75 KV |
| Collision Energy: | 10-35, ramp |
| Collision Gas: | N2 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 325°C |
| Fragmentation Method: | CID |
| Ionization: | ES+ |
| Mass Accuracy: | 5ppm |
| Dataformat: | Profile |
| Desolvation Gas Flow: | 45 |
| Desolvation Temperature: | 325°C |
| Resolution Setting: | 120000 |
| Scan Range Moverz: | 70-1050 m/z |
| Scanning Range: | 70-1050 m/z |
