{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003107","ANALYSIS_ID":"AN005086","VERSION":"1","CREATED_ON":"03-06-2024"},

"PROJECT":{"PROJECT_TITLE":"FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma","PROJECT_SUMMARY":"Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to FGFR inhibitor treatment. However, the depth and duration of responses are often limited. Here, we conducted integrative transcriptomics, metabolomics, and phosphoproteomics analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. We find FGFR2-mediated activation of NF-kB maintains a highly glycolytic phenotype. Conversely, FGFR inhibition blocks glucose uptake and glycolysis while inciting a series of adaptive changes, including switching fuel source utilization to favor fatty acid oxidation and increasing mitochondrial fusion and autophagy. Accordingly, FGFR inhibitor efficacy is potentiated by combined mitochondrial targeting, an effect enhanced in xenograft models by intermittent fasting. Thus, we show that oncogenic FGFR2 signaling drives NF-kB-dependent glycolysis in ICC and that metabolic reprogramming in response to FGFR inhibition confers new targetable vulnerabilities.","INSTITUTE":"mgh","LAST_NAME":"Zhen","FIRST_NAME":"Yuanli","ADDRESS":"185 cambridge street, room 4100","EMAIL":"yzhen1@mgh.harvard.edu","PHONE":"4698792279"},

"STUDY":{"STUDY_TITLE":"Characterization of metabolic changes upon FGFR inhibition in ICC13-7 Xenograft","STUDY_SUMMARY":"Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to treatment with FGFR inhibitors. However, the depth and duration of responses are often limited. Here, we conducted integrative transcriptomic and metabolomic analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. We find FGFR2-mediated activation of NF-B maintains a highly glycolytic phenotype. Conversely, FGFR inhibition blocks glucose uptake and glycolysis while inciting a series of adaptive changes, including switching fuel source utilization to favor fatty acid oxidation and increasing mitochondrial fusion and autophagy. Accordingly, FGFR inhibitor efficacy is potentiated by combined mitochondrial targeting, an effect enhanced in xenograft models by intermittent fasting. Thus, we show that oncogenic FGFR2 signaling drives NF-B-dependent glycolysis in ICC and that metabolic reprogramming in response to FGFR inhibition confers new targetable vulnerabilities.","INSTITUTE":"Massachusetts General Hospital","LAST_NAME":"Zhen","FIRST_NAME":"Yuanli","ADDRESS":"185 cambridge street, room 4100","EMAIL":"yzhen1@mgh.harvard.edu","PHONE":"4698792279","SUBMIT_DATE":"2024-01-17"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL06",
"Factors":{"treatment":"Pemigatinib","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL06"}
},
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL07",
"Factors":{"treatment":"Pemigatinib","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL07"}
},
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL08",
"Factors":{"treatment":"Pemigatinib","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL08"}
},
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL02",
"Factors":{"treatment":"Vehicle","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL02"}
},
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL03",
"Factors":{"treatment":"Vehicle","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL03"}
},
{
"Subject ID":"-",
"Sample ID":"SUB13746p4_SPL04",
"Factors":{"treatment":"Vehicle","Sample source":"ICC13-7 Xenograft"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"SUB13746p4_SPL04"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Tumors were collected and snap-frozen in liquid N2","SAMPLE_TYPE":"ICC13-7 xenograft"},

"TREATMENT":{"TREATMENT_SUMMARY":"ICC13-7 xenografts were treated with vehicle vs Pemigatinib(1mg/kg) for 7 days. On the day7, collect tumor 4h after last dose of treatment (vehicle vs 1mg/kg pemigatinib)."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extractions were conducted following the biphasic extraction protocol. Basically, add cold chloroform to samples (in methanol) with a ratio of 2:1. Vortex samples for 1 minute to homogenize. Add 1 fraction of water, and vortex samples again. Glass vials were centrifuged at 3000 rcf for 10 minutes for phase separation. The aqueous phase was transferred to a new glass vial for metabolomics and the remaining interphase was used for protein quantification. The aqueous phase was evaporated under nitrogen flow. Samples were resuspended in 50% acetonitrile, and the volume was scaled according to the protein amounts. 15ul was used for the lowest biomass, and all others were scaled accordingly. Standard mixes were prepared at 100 uM and run after the samples to allow for the identification of the targets."},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)","COLUMN_TEMPERATURE":"40","FLOW_GRADIENT":"Started at 93% B/7% A; 40% B/60% A in 19 min; 100% A in 9 min; 100% A for 5 min; back to 93% B/7% A in 3 min and re-equilibration at 93% B/7% A for 9 min.","FLOW_RATE":"0.05 to 0.15 mL/min in 30 seconds uniformly; then held at 0.15 mL/min.","SOLVENT_A":"100% Water; 20 mMAmmonium Carbonate, 0.1% Ammonium hydroxide","SOLVENT_B":"Acetonitrile 97%, 3% water","CHROMATOGRAPHY_TYPE":"HILIC"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap ID-X tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Data was acquired on the ID-X in switching polarities at 120000 resolution, with an AGC target of 1e5, and a m/z range of 65 to 1000. MS1 data is acquired in switching polarities for all samples. Data is analyzed in Compound Discoverer 3.3 (CD, ThermoFisher Scientific). A mix of standard of each target was run along the samples and used as the unlabeled reference for the CD labelling workflow. Isotopomer distribution is found in the exchange column, as % of 0 labelled carbon, 1 labelled carbon, 2 labelled carbon, etc. Those are corrected for natural abundance. For the compounds that couldn’t be analyzed by CD, the areas have been extracted with Tracefinder manually.","ION_MODE":"UNSPECIFIED"},

"MS_METABOLITE_DATA":{
"Units":"area analyzed by Compound Discoverer (counts x seconds)",

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SPL03":"22400000000.0000","SUB13746p4_SPL04":"22600000000.0000"},{"Metabolite":"CTP","SUB13746p4_SPL06":"35700000.0000","SUB13746p4_SPL07":"29000000.0000","SUB13746p4_SPL08":"11700000.0000","SUB13746p4_SPL02":"20000000.0000","SUB13746p4_SPL03":"32800000.0000","SUB13746p4_SPL04":"47200000.0000"},{"Metabolite":"Cysteine","SUB13746p4_SPL06":"","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"","SUB13746p4_SPL03":"","SUB13746p4_SPL04":""},{"Metabolite":"Cystine","SUB13746p4_SPL06":"","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"","SUB13746p4_SPL03":"","SUB13746p4_SPL04":""},{"Metabolite":"cytosine","SUB13746p4_SPL06":"190000000.0000","SUB13746p4_SPL07":"228000000.0000","SUB13746p4_SPL08":"215000000.0000","SUB13746p4_SPL02":"265000000.0000","SUB13746p4_SPL03":"202000000.0000","SUB13746p4_SPL04":"244000000.0000"},{"Metabolite":"d-ADP","SUB13746p4_SPL06":"","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"","SUB13746p4_SPL03":"","SUB13746p4_SPL04":""},{"Metabolite":"d-AMP","SUB13746p4_SPL06":"2280000.0000","SUB13746p4_SPL07":"1730000.0000","SUB13746p4_SPL08":"1270000.0000","SUB13746p4_SPL02":"6090000.0000","SUB13746p4_SPL03":"2530000.0000","SUB13746p4_SPL04":"1870000.0000"},{"Metabolite":"dATP","SUB13746p4_SPL06":"37100.0000","SUB13746p4_SPL07":"105000.0000","SUB13746p4_SPL08":"12100.0000","SUB13746p4_SPL02":"141000.0000","SUB13746p4_SPL03":"234000.0000","SUB13746p4_SPL04":"320000.0000"},{"Metabolite":"d-CDP","SUB13746p4_SPL06":"119000.0000","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"323000.0000","SUB13746p4_SPL03":"102000.0000","SUB13746p4_SPL04":"237000.0000"},{"Metabolite":"d-CMP","SUB13746p4_SPL06":"3490000.0000","SUB13746p4_SPL07":"596000.0000","SUB13746p4_SPL08":"1470000.0000","SUB13746p4_SPL02":"1330000.0000","SUB13746p4_SPL03":"1200000.0000","SUB13746p4_SPL04":"1940000.0000"},{"Metabolite":"dCTP","SUB13746p4_SPL06":"330000.0000","SUB13746p4_SPL07":"265000.0000","SUB13746p4_SPL08":"169000.0000","SUB13746p4_SPL02":"361000.0000","SUB13746p4_SPL03":"363000.0000","SUB13746p4_SPL04":"500000.0000"},{"Metabolite":"d-GDP","SUB13746p4_SPL06":"","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"","SUB13746p4_SPL03":"","SUB13746p4_SPL04":""},{"Metabolite":"d-GMP","SUB13746p4_SPL06":"45000000.0000","SUB13746p4_SPL07":"38800000.0000","SUB13746p4_SPL08":"31600000.0000","SUB13746p4_SPL02":"36400000.0000","SUB13746p4_SPL03":"40300000.0000","SUB13746p4_SPL04":"43400000.0000"},{"Metabolite":"dGTP","SUB13746p4_SPL06":"","SUB13746p4_SPL07":"","SUB13746p4_SPL08":"","SUB13746p4_SPL02":"","SUB13746p4_SPL03":"","SUB13746p4_SPL04":""},{"Metabolite":"Dihydrouracil","SUB13746p4_SPL06":"6480000.0000","SUB13746p4_SPL07":"6180000.0000","SUB13746p4_SPL08":"6500000.0000","SUB13746p4_SPL02":"11000000.0000","SUB13746p4_SPL03":"9430000.0000","SUB13746p4_SPL04":"11900000.0000"},{"Metabolite":"dTTP","SUB13746p4_SPL06":"390000.0000","SUB13746p4_SPL07":"410000.0000","SUB13746p4_SPL08":"302000.0000","SUB13746p4_SPL02":"827000.0000","SUB13746p4_SPL03":"1020000.0000","SUB13746p4_SPL04":"1000000.0000"},{"Metabolite":"Erythrose 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