{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001670","ANALYSIS_ID":"AN002726","VERSION":"1","CREATED_ON":"February 1, 2021, 2:22 pm"},

"PROJECT":{"PROJECT_TITLE":"Reinforcing one-carbon metabolism via folic acid/Folr1 promotes beta-cell formation","PROJECT_SUMMARY":"Diabetes can be caused by an insufficient beta-cell mass. Here, we performed a genetic screen in a zebrafish model with beta-cell loss to identify pathways promoting beta-cell regeneration. We found that both folate receptor 1 (folr1) overexpression and treatment with folate intermediates, i.e. tetrahydrofolic acid (THF) or folinic acid stimulated beta-cell differentiation in zebrafish. Treatment with these folate intermediates also stimulated beta-cell differentiation in neonatal pig islet cultures, showing the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets, the increased beta-cell differentiation originated from ductal cells. Mechanistically, comparative metabolomics analyses of zebrafish in the basal state vs following -cell ablation and in un-treated vs folinic acid-treated zebrafish indicated beta-cell regeneration could be attributed to changes in the pyrimidine, carnitine and serine pathways. Overall, our results suggest evolutionary conserved and previously unknown roles of folic acid and one-carbon metabolism in the generation of beta-cell .","INSTITUTE":"North Carolina State University","DEPARTMENT":"Molecular and Structural Biochemistry","LAST_NAME":"Duan","FIRST_NAME":"Likun","ADDRESS":"120 W Broughton Dr.","EMAIL":"lduan2@ncsu.edu","PHONE":"9195939853"},

"STUDY":{"STUDY_TITLE":"Metabolomics characterization of zebrafish larvae","STUDY_TYPE":"MS analysis","STUDY_SUMMARY":"Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment.","INSTITUTE":"North Carolina State University","DEPARTMENT":"Molecular and Structural Biochemistry","LAST_NAME":"Duan","FIRST_NAME":"Likun","ADDRESS":"120 W Broughton Dr.","EMAIL":"lduan2@ncsu.edu","PHONE":"9195939853"},

"SUBJECT":{"SUBJECT_TYPE":"Fish","SUBJECT_SPECIES":"Danio rerio","TAXONOMY_ID":"7955"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"NA",
"Sample ID":"AA 02030 metabo control 001",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"AA 02030 metabo control 001","sample name(backup)":"ND+MTZ-control A2"}
},
{
"Subject ID":"NA",
"Sample ID":"AA 02030 metabo control 002",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"AA 02030 metabo control 002","sample name(backup)":"ND+MTZ-control A3"}
},
{
"Subject ID":"NA",
"Sample ID":"AA 02030 metabo control 003",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"AA 02030 metabo control 003","sample name(backup)":"ND+MTZ-control A4"}
},
{
"Subject ID":"NA",
"Sample ID":"AA 02030 metabo control 004",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"AA 02030 metabo control 004","sample name(backup)":"ND+MTZ-control A5"}
},
{
"Subject ID":"NA",
"Sample ID":"AA 02030 metabo control 005",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"AA 02030 metabo control 005","sample name(backup)":"ND+MTZ-control A6"}
},
{
"Subject ID":"NA",
"Sample ID":"BB 02030 metabo FA 001",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"BB 02030 metabo FA 001","sample name(backup)":"ND+MTZ-Folinic acid B2"}
},
{
"Subject ID":"NA",
"Sample ID":"BB 02030 metabo FA 002",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"BB 02030 metabo FA 002","sample name(backup)":"ND+MTZ-Folinic acid B3"}
},
{
"Subject ID":"NA",
"Sample ID":"BB 02030 metabo FA 003",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"BB 02030 metabo FA 003","sample name(backup)":"ND+MTZ-Folinic acid B4"}
},
{
"Subject ID":"NA",
"Sample ID":"BB 02030 metabo FA 004",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"BB 02030 metabo FA 004","sample name(backup)":"ND+MTZ-Folinic acid B5"}
},
{
"Subject ID":"NA",
"Sample ID":"BB 02030 metabo FA 005",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"BB 02030 metabo FA 005","sample name(backup)":"ND+MTZ-Folinic acid B6"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 001",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  001","sample name(backup)":"Reg+MTZ-control C1"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 002",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  002","sample name(backup)":"Reg+MTZ-control C2"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 003",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  003","sample name(backup)":"Reg+MTZ-control C3"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 004",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  004","sample name(backup)":"Reg+MTZ-control C4"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 005",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  005","sample name(backup)":"Reg+MTZ-control C5"}
},
{
"Subject ID":"Regulation",
"Sample ID":"CC 02030 metabo reg control 006",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"CC 02030 metabo reg control  006","sample name(backup)":"Reg+MTZ-control C6"}
},
{
"Subject ID":"Regulation",
"Sample ID":"DD 02030 metabo reg FA 001",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"DD 02030 metabo reg FA 001","sample name(backup)":"Reg+MTZ-Folinic acid D2"}
},
{
"Subject ID":"Regulation",
"Sample ID":"DD 02030 metabo reg FA 002",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"DD 02030 metabo reg FA 002","sample name(backup)":"Reg+MTZ-Folinic acid D3"}
},
{
"Subject ID":"Regulation",
"Sample ID":"DD 02030 metabo reg FA 003",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"DD 02030 metabo reg FA 003","sample name(backup)":"Reg+MTZ-Folinic acid D4"}
},
{
"Subject ID":"Regulation",
"Sample ID":"DD 02030 metabo reg FA 004",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"DD 02030 metabo reg FA 004","sample name(backup)":"Reg+MTZ-Folinic acid D5"}
},
{
"Subject ID":"Regulation",
"Sample ID":"DD 02030 metabo reg FA 005",
"Factors":{"Treatment":"Folinic acid"},
"Additional sample data":{"RAW_FILE_NAME":"DD 02030 metabo reg FA 005","sample name(backup)":"Reg+MTZ-Folinic acid D6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details.","SAMPLE_TYPE":"Larvae"},

"TREATMENT":{"TREATMENT_SUMMARY":"Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Metabolites were extracted from 5 pooled larvae, and 6 replicates were used per condition. Metabolites were extracted as described previously36. Some of the replicates were used to optimize the analysis of polar metabolites and folate derivatives using Vanquish UHPLC (Thermo Fisher Scientific). Please refer to the publication for more details."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The analysis of folic acid and its derivatives was performed using Luna column (100 x 3 mm i.d., 3 µm, C18(2), 100 Å, Phenomenex) at 25 °C. Mobile phase A: water with 0.1% formic acid, and mobile phase B: 100 % methanol. Linear gradient was: 0 min, 2% B; 1.5 min, 2% B; 3.0 min, 15% B; 5.5 min, 95% B; 14.5 min, 95% B; 15.0 min, 2% B; 22.0 min, 2% B. The flow rate was 0.150 ml/min.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish UHPLC","COLUMN_NAME":"Luna C18 LC (150 x 4.6 mm, 3µm)","CHROMATOGRAPHY_COMMENTS":"Luna® 3 µm C18(2) 100 Å, LC Column 150 x 4.6 mm, Ea"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap Exploris 480","INSTRUMENT_TYPE":"Ion trap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Xcalibur 4.4 from Thermo Scientific for data acquisition and we use Sieve 2.2 for chromatographic alignment and peak integration.To measure folate derivatives, Orbitrap Exploris 480 was operated in SIM mode (selected ion monitoring) targeting the following ions: folic acid (442.1470), 5-methyltetrahydrofolate (460.1939), and folinic acid (474.1732)."},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"Folate","AA 02030 metabo control 001":"63243","AA 02030 metabo control 002":"103420","AA 02030 metabo control 003":"83131","AA 02030 metabo control 004":"82691","AA 02030 metabo control 005":"84651","BB 02030 metabo FA 001":"93701","BB 02030 metabo FA 002":"43257","BB 02030 metabo FA 003":"42328","BB 02030 metabo FA 004":"50610","BB 02030 metabo FA 005":"44157","CC 02030 metabo reg control 001":"104392","CC 02030 metabo reg control 002":"49820","CC 02030 metabo reg control 003":"81253","CC 02030 metabo reg control 004":"58467","CC 02030 metabo reg control 005":"60879","CC 02030 metabo reg control 006":"54007","DD 02030 metabo reg FA 001":"74655","DD 02030 metabo reg FA 002":"66689","DD 02030 metabo reg FA 003":"58274","DD 02030 metabo reg FA 004":"52330","DD 02030 metabo reg FA 005":"65491"},{"Metabolite":"Folinic acid","AA 02030 metabo control 001":"84996","AA 02030 metabo control 002":"36087","AA 02030 metabo control 003":"25231","AA 02030 metabo control 004":"51105","AA 02030 metabo control 005":"76171","BB 02030 metabo FA 001":"1006124","BB 02030 metabo FA 002":"185766","BB 02030 metabo FA 003":"268170","BB 02030 metabo FA 004":"159763","BB 02030 metabo FA 005":"227629","CC 02030 metabo reg control 001":"33254","CC 02030 metabo reg control 002":"58233","CC 02030 metabo reg control 003":"97169","CC 02030 metabo reg control 004":"62200","CC 02030 metabo reg control 005":"77590","CC 02030 metabo reg control 006":"25840","DD 02030 metabo reg FA 001":"411439","DD 02030 metabo reg FA 002":"173715","DD 02030 metabo reg FA 003":"174951","DD 02030 metabo reg FA 004":"201294","DD 02030 metabo reg FA 005":"242931"},{"Metabolite":"5-Methyltetrahydrofolate","AA 02030 metabo control 001":"56669","AA 02030 metabo control 002":"80299","AA 02030 metabo control 003":"90421","AA 02030 metabo control 004":"85669","AA 02030 metabo control 005":"91775","BB 02030 metabo FA 001":"68142","BB 02030 metabo FA 002":"71676","BB 02030 metabo FA 003":"78651","BB 02030 metabo FA 004":"81315","BB 02030 metabo FA 005":"65435","CC 02030 metabo reg control 001":"102019","CC 02030 metabo reg control 002":"86394","CC 02030 metabo reg control 003":"86782","CC 02030 metabo reg control 004":"92486","CC 02030 metabo reg control 005":"100866","CC 02030 metabo reg control 006":"65445","DD 02030 metabo reg FA 001":"123958","DD 02030 metabo reg FA 002":"103408","DD 02030 metabo reg FA 003":"103228","DD 02030 metabo reg FA 004":"83485","DD 02030 metabo reg FA 005":"68143"}],

"Metabolites":[{"metabolite_name":"Folate"},{"metabolite_name":"Folinic acid"},{"metabolite_name":"5-Methyltetrahydrofolate"}]
}

}