{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001266","ANALYSIS_ID":"AN002103","VERSION":"1","CREATED_ON":"October 15, 2019, 12:34 pm"},

"PROJECT":{"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"},

"STUDY":{"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 at Chapel Hill","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"500 Laureate Way, Kannapolis, NC 28081","EMAIL":"Susan_sumner@unc.edu","PHONE":"(919)6224456"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","CELL_STRAIN_DETAILS":"INS-1 832/13 cell line"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CB_1",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_10",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_11",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_12",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_13",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_14",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_15",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_16",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_17",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_18",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_19",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_2",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_20",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_21",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_22",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_23",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_24",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_25",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_26",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_27",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_28",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_29",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_3",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_30",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_31",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_32",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_33",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_34",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_35",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"monomethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_36",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_37",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_38",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_39",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_4",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_40",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"dimethylated arsenic"}
},
{
"Subject ID":"-",
"Sample ID":"CB_5",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"No treatment"}
},
{
"Subject ID":"-",
"Sample ID":"CB_6",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_7",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_8",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"CB_9",
"Factors":{"Cell Type":"INS-1 (beta cells)","Treatment":"inorganic arsenic (sodium arsenite)"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_1_1",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_1_2",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_2_1",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_2_2",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_3_1",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_3_2",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CB_4",
"Factors":{"Cell Type":"Beta cell sample pool","Treatment":"-"}
}
],
"COLLECTION":{"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_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"},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","FLOW_RATE":"0.4 ml/min","COLUMN_TEMPERATURE":"50","SOLVENT_A":"Water with 0.1% Formic Acid","SOLVENT_B":"Methanol with 0.1% Formic Acid","COLUMN_PRESSURE":"6000-10000 psi","INJECTION_TEMPERATURE":"8","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"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"UNC-NRI Sumner Lab","OPERATOR_NAME":"Yuanyuan Li","DETECTOR_TYPE":"Orbitrap","SOFTWARE_VERSION":"Xcalibur 4.1","DATA_FORMAT":"profile"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"We used DDA mode to acquire the MS and MS/MS data. Progenesis QI was used for peak picking, alignment, and normalization.","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","MS_RESULTS_FILE":"ST001266_AN002103_Results.txt UNITS:Relative Intensity Has m/z:Yes Has RT:Yes RT units:Minutes"}

}