{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003102","ANALYSIS_ID":"AN005076","VERSION":"1","CREATED_ON":"05-28-2024"},

"PROJECT":{"PROJECT_TITLE":"Cellular adaptation to cancer therapy along a resistance continuum","PROJECT_SUMMARY":"Recent research has shed light on the role of non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell state transitions occurring in the adaptation to cancer therapies remain elusive and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell state transitions accompanied by a progressive increase in cell fitness, which we denote the ‘resistance continuum’. This cellular adaptation involves a step-wise assembly of gene expression programs and epigenetically reinforced cell states underpinned by phenotypic plasticity stress adaptation and metabolic reprogramming. Through systematic genetic perturbations, we identify an acquisition of progressive metabolic dependencies, exposing a spectrum of vulnerabilities that can be potentially exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell state transitions.","INSTITUTE":"NYU Langone Health","LAST_NAME":"Starvaggi Franca","FIRST_NAME":"Gustavo","ADDRESS":"430 E 29th Street","EMAIL":"Gustavo.StarvaggiFranca@nyulangone.org","PHONE":"646-501-4603","FUNDING_SOURCE":"NIH grants: P50 CA225450","DOI":"http://dx.doi.org/10.21228/M8WM7T"},

"STUDY":{"STUDY_TITLE":"Cellular adaptation to cancer therapy along a resistance continuum","STUDY_SUMMARY":"Recent research has shed light on the role of non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell state transitions occurring in the adaptation to cancer therapies remain elusive and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell state transitions accompanied by a progressive increase in cell fitness, which we denote the ‘resistance continuum’. This cellular adaptation involves a step-wise assembly of gene expression programs and epigenetically reinforced cell states underpinned by phenotypic plasticity stress adaptation and metabolic reprogramming. Through systematic genetic perturbations, we identify an acquisition of progressive metabolic dependencies, exposing a spectrum of vulnerabilities that can be potentially exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell state transitions.","INSTITUTE":"NYU Langone Health","LAST_NAME":"Starvaggi Franca","FIRST_NAME":"Gustavo","ADDRESS":"430 East 29th Street, NY NY 10016","EMAIL":"Gustavo.StarvaggiFranca@nyulangone.org","PHONE":"6465015151","SUBMIT_DATE":"2024-02-13"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"C_1",
"Sample ID":"S25059",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25059.mzXML"}
},
{
"Subject ID":"C_2",
"Sample ID":"S25060",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25060.mzXML"}
},
{
"Subject ID":"C_3",
"Sample ID":"S25061",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25061.mzXML"}
},
{
"Subject ID":"C_1_drug",
"Sample ID":"S25062",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25062.mzXML"}
},
{
"Subject ID":"C_2_drug",
"Sample ID":"S25063",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25063.mzXML"}
},
{
"Subject ID":"C_3_drug",
"Sample ID":"S25064",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"C_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25064.mzXML"}
},
{
"Subject ID":"T320_1",
"Sample ID":"S25065",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25065.mzXML"}
},
{
"Subject ID":"T320_2",
"Sample ID":"S25066",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25066.mzXML"}
},
{
"Subject ID":"T320_3",
"Sample ID":"S25067",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25067.mzXML"}
},
{
"Subject ID":"T320_1_drug",
"Sample ID":"S25068",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25068.mzXML"}
},
{
"Subject ID":"T320_2_drug",
"Sample ID":"S25069",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25069.mzXML"}
},
{
"Subject ID":"T320_3_drug",
"Sample ID":"S25070",
"Factors":{"Sample source":"Ovarian cancer cells","Treatment":"T320_drug"},
"Additional sample data":{"RAW_FILE_NAME":"SQ1169/S25070.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"To generate drug-induced PARPi resistant populations, 1×106 Kuramochi drug-naïve cells (C) were initially seeded in 150 mm plates.","SAMPLE_TYPE":"Ovarian cancer cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Twenty four hours after seeding, 1 uM of olaparib (Selleckchem, S1060) was added and cells were maintained under treatment until reaching confluency (> 70%), thus characterizing resistance at this dose. Cells were harvested (0.25% Trypsin/EDTA for 5 min at 37°C) and a fraction of the surviving population (1×106 cells) was seeded again and treated with 2.5 uM until cells reached confluency. This process was repeated sequentially by doubling the drug concentrations until the cell populations were able to achieve confluency at 320 uM of olaparib (T320). The initial dose was determined by cell viability assays, indicating a low starting dose (< IC30). At each step, aliquots of the adapted populations were frozen (10% DMSO, 50% FBS, 40% media) for further experiments"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Kuramochi cells (C and T320) were cultured until ~80% confluence either on 320 uM of olaparib for 24h or off treatment in triplicates per condition. Cell pellets were collected and frozen with liquid nitrogen for submission to the NYU Metabolomics Core Resource Laboratory. Samples were subjected to an LCMS analysis to detect and quantify known peaks. A metabolite extraction was carried out on each sample based on a previously described method116."},

"CHROMATOGRAPHY":{"METHODS_FILENAME":"L12","CHROMATOGRAPHY_COMMENTS":"The LC column was a MilliporeTM ZIC-pHILIC (2.1 x150 mm, 5 μm) coupled to a Dionex Ultimate 3000TM system and the column oven temperature was set to 25oC for the gradient elution. A flow rate of 100 μL/min was used with the following buffers; A) 10 mM ammonium carbonate in water, pH 9.0, and B) neat acetonitrile. The gradient profile was as follows; 80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min). Injection volume was set to 2 μL for all analyses (42 min total run time per injection).","INSTRUMENT_NAME":"Ulitmate 3000","COLUMN_NAME":"SeQuant ZIC-pHILIC (150 x 4.6mm,5um)","COLUMN_PRESSURE":"1800","COLUMN_TEMPERATURE":"25","FLOW_GRADIENT":"80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min)","FLOW_RATE":"0.1mL/min","INJECTION_TEMPERATURE":"4","INTERNAL_STANDARD":"ISTD (500nM amino acid cocktail)","SAMPLE_INJECTION":"2uL","SOLVENT_A":"100% water; 10 mM ammonium carbonate, pH 9.0","SOLVENT_B":"100% acetonitrile","ANALYTICAL_TIME":"30m","OVEN_TEMPERATURE":"28","CHROMATOGRAPHY_TYPE":"HILIC"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","MS_COMMENTS":"M.13 Polar metabolites (pHILIC Hybrid). MS analyses were carried out by coupling the LC system to a Thermo Q Exactive HFTM mass spectrometer operating in heated electrospray ionization mode (HESI). Method duration was 30 min with a polarity switching data-dependent Top 5 method for both positive and negative modes. Spray voltage for both positive and negative modes was 3.5kV and capillary temperature was set to 320oC with a sheath gas rate of 35, aux gas of 10, and max spray current of 100 μA. The full MS scan for both polarities utilized 120,000 resolution with an AGC target of 3e6 and a maximum IT of 100 ms, and the scan range was from 67-1000 m/z. Tandem MS spectra for both positive and negative mode used a resolution of 15,000, AGC target of 1e5, maximum IT of 50 ms, isolation window of 0.4 m/z, isolation offset of 0.1 m/z, fixed first mass of 50 m/z, and 3-way multiplexed normalized collision energies (nCE) of 10, 35, 80. The minimum AGC target was 1e4 with an intensity threshold of 2e5. All data were acquired in profile mode.","ION_MODE":"UNSPECIFIED"},

"MS_METABOLITE_DATA":{
"Units":"Arbitrary units",

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