{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001314","ANALYSIS_ID":"AN002188","VERSION":"1","CREATED_ON":"February 3, 2020, 2:24 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, Islets (part-II)","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 islets are a primary target for iAs and its metabolites and that impaired insulin secretion by islets 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","GENDER":"Male","CELL_PRIMARY_IMMORTALIZED":"Islets isolated from pancreata of adult C57BL/J6 male mice","CELL_COUNTS":"100 islets"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CI_29",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_29.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_22",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_22.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_15",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_15.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_33",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_33.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_14",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_14.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_20",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_20.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_17",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_17.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_19",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_19.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_36",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_36.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_21",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_21.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_8",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_8.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_39",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_39.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_38",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_38.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_3",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_3.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_40",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_40.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_27",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_27.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_6",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_6.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_9",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_9.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_18",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_18.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_35",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_35.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_23",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_23.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_25",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_25.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_32",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_32.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_13",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_13.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_37",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_37.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_26",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_26.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_2",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_2.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_12",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_12.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_11",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_11.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_34",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_34.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_31",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_31.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_10",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_10.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_28",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_28.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_1",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_1.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_24",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_24.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_5",
"Factors":{"Cell type":"Islet","Treatment":"No treatment"},
"Additional sample data":{"RAW_FILE_NAME":"CI_5.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_30",
"Factors":{"Cell type":"Islet","Treatment":"inorganic arsenic (sodium arsenite)"},
"Additional sample data":{"RAW_FILE_NAME":"CI_30.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_16",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_16.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_7",
"Factors":{"Cell type":"Islet","Treatment":"monomethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_7.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"CI_4",
"Factors":{"Cell type":"Islet","Treatment":"dimethylated arsenic"},
"Additional sample data":{"RAW_FILE_NAME":"CI_4.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_1_1",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_1_1.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_1_2",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_1_2.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_2_1",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_2_1.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_2_2",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_2_2.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_3_1",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_3_1.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_3_2",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_3_2.RAW"}
},
{
"Subject ID":"-",
"Sample ID":"SP_CL_4",
"Factors":{"Cell type":"Islet sample pool","Treatment":"Islet sample pool"},
"Additional sample data":{"RAW_FILE_NAME":"SP_CL_4.RAW"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Pancreatic islets were isolated from adult male C57BL/6 mice (Charles River Laboratories, Wilmington, MA). All procedures involving mice were approved by the University of North Carolina Institutional Animal and Use Committee. Mice were sacrificed by cervical dislocation and pancreas was infused in situwith collagenase P (1 mg/ml, Roche Diagnostics Corp., Indianapolis, IN) via the common bile duct. Pancreas was then removed and digested in the collagenase solution for 12 min at 37 °C. The digestate was washed and islets were purified by centrifugation in a gradient of Ficoll PM 400 (GE Healthcare, Uppsala, Sweden) (Szot et al., 2007).The isolated islets were cultivated overnight at 37 °C with 5% CO2 in RPMI 1640 medium (Mediatech, Manassas, VA) with 10% fetal bovine serum, 10 mM Hepes, 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin (all from Sigma-Aldrich, St. Louis, MO). The same medium was used in experiments in which the islets were exposed to iAsIII (sodium arsenite; Sigma-Aldrich), MAsIII(methylarsine oxide) or DMAsIII (iododimethylarsine).","SAMPLE_TYPE":"Pancreas","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"The isolated islets were incubated overnight at 37°C with 5% CO2 at 6-well plates in RPMI 1640 medium with 10% fetal bovine serum, 10 mM HEPES, 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin (all from Gibco). The islets were then exposed to 2 μM iAsIII, 0.25 μM MAsIII, or 0.5 μM DMAsIII for 48 hours. Control islets were incubated in the culture medium without arsenicals.","CELL_STORAGE":"-80 °C"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"With a randomized order, islet samples were put on dry ice before sample preparation. A volume of 400 uL ice cold methanol-water (80:20) was added, and then vortex for 5 min at 5000 rpm. All contents in the tube were transferred into pre-labeled MagNaLyzer tubes (with 10-15 beads inside). The tubes were put on 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 20 min at 4°C. A volume of 300 µl supernatant were transferred into pre-labeled 1.5 ml Low-bind Eppendorf tube. For quality control purpose, 32 µl of the supernatant from individual sample was transferred and mixed in new 2-ml tube to make a sample pool (SP). A volume of 300 µl SP was transferred into a pre-labeled 2.0 ml Low-bind Eppendorf tubes. All samples, including study samples and pools, were dried under speed-vac. For immediate analysis, 100 µL of Water-Methanol (95:5) containing 500 ng/mL L-tryphtophan-d5 was added to the residue, and then vortexed 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":"ST001314_AN002188_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}