{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002720","ANALYSIS_ID":"AN004410","VERSION":"1","CREATED_ON":"May 30, 2023, 1:24 am"},

"PROJECT":{"PROJECT_TITLE":"Biochemical Impact of Platinum and Palladium-based Anticancer Agents – BioIMPACT","PROJECT_TYPE":"NMR-based metabolomics","PROJECT_SUMMARY":"Platinum (Pt(II)) drugs, e.g. cisplatin (cDDP), are some of the most used chemotherapeutic agents, yet tumor acquired resistance and high toxicity are still current drawbacks. Palladium (Pd(II))-complexes are alternatives due to similar metal coordination and promising cytotoxic properties. Metabolomics can measure the metabolic response of both drug-exposed cells and tissues, unveiling insight into drug mechanisms and metabolic markers of drug efficacy, toxicity and resistance. The present 1H NMR metabolomics study aims to (i) describe the endometabolome of both MDA-MB-231 parental and cDDP-resistant cells (MDA-MB-231R), which are representative of Triple-Negative Breast Cancer, and (ii) characterize the metabolic profile of both cell types exposed to the novel Pd(II)-spermine complex (Pd2Spm), in comparison with cDDP signature, describing possible biomarker patterns of tumor resistance and therapy response.","INSTITUTE":"University of Aveiro","DEPARTMENT":"Department of Chemistry and CICECO-Aveiro Institute of Materials","LABORATORY":"Metabolomics from Ana M. Gil","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana J.","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351926369478","FUNDING_SOURCE":"This work was developed within the CICECO-Aveiro Institute of Materials project (UIDB/50011/2020, UIDP/50011/2020 & LA/P/0006/2020) financed by national funds through the FCT/MTES (PIDDAC). We also acknowledge funds from POCentro, Portugal 2020 and European Community through the FEDER and by the Portuguese Foundation for Science and Technology (FCT) through LAQV/REQUIMTE FCT UIDB/50006/2020 (C.D.), UIDB/00070/2020 (A.L.M.B.d.C. and M.P.M.M.) and POCI-01-0145-FEDER-0016786. We are grateful to the Portuguese National NMR Network (PTNMR), supported by FCT funds as the NMR spectrometer used is part of PTNMR and partially supported by Infrastructure Project No. 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL, and the FCT through PIDDAC). T.J.C. thanks FCT for her Ph.D. grant SFRH/BD/145920/2019 and M.V. thanks the FCT and the Ph.D. Program in Med-icines and Pharmaceutical Innovation (i3DU) for his Ph.D. grant PD/BD/135460/2017; both grants were funded by the European Social Fund of the European Union and national FCT/MCTES funds."},

"STUDY":{"STUDY_TITLE":"Metabolic characterization of the polar endometabolome of Triple-Negative Breast Cancer parental and cDDP-resistant cells","STUDY_TYPE":"NMR-based metabolomics","STUDY_SUMMARY":"Platinum (Pt(II)) drugs, e.g. cisplatin (cDDP), are some of the most used chemotherapeutic agents, yet tumor acquired resistance and high toxicity are still current drawbacks. Metabolomics can measure the metabolic response of drug-exposed cells, unveiling insight into drug mechanisms and metabolic markers of drug efficacy, toxicity and resistance. The present 1H NMR metabolomics study aims to describe the polar endometabolome of both MDA-MB-231 parental and cDDP-resistant cells (MDA-MB-231R), which are representative of Triple-Negative Breast Cancer, aiding the current knowledge about the resistant cells metabolism rewiring and disclosing metabolic hotspots as possible targets to counteract the therapy resistance.","INSTITUTE":"University of Aveiro","DEPARTMENT":"Department of Chemistry and CICECO-Aveiro Institute of Materials","LABORATORY":"Metabolomics from Ana M. Gil","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana João","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351926369478","NUM_GROUPS":"6"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENOTYPE_STRAIN":"MDA-MB-231 cells","GENDER":"Not applicable","CELL_BIOSOURCE_OR_SUPPLIER":"ATCC (Manassas, VA, USA); ATCC HTB-26","CELL_STRAIN_DETAILS":"Epithelial breast cancer cells; absence of estrogen and progesterone receptors, HER2 overexpression","CELL_PASSAGE_NUMBER":"Between 5 to 10","CELL_COUNTS":"5 M"},
"SUBJECT_SAMPLE_FACTORS":[
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"Subject ID":"-",
"Sample ID":"R_C0h_EA_11_1_2",
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{
"Subject ID":"-",
"Sample ID":"R_C0h_EA_12_1_2",
"Factors":{"Treatment_group":"Resistant_Controls_0h"},
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"Sample ID":"R_C48h_EA_31_1_2",
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"Subject ID":"-",
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{
"Subject ID":"-",
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{
"Subject ID":"-",
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{
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{
"Subject ID":"-",
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{
"Subject ID":"-",
"Sample ID":"S_C0h_EA_31_1_2",
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{
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"Subject ID":"-",
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{
"Subject ID":"-",
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{
"Subject ID":"-",
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"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
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{
"Subject ID":"-",
"Sample ID":"S_C24h_EA_13_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_13_1_2"}
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{
"Subject ID":"-",
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"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_21_1_2"}
},
{
"Subject ID":"-",
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"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_22_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C24h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C24h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_31_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C24h_EA_32_1_2",
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"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_32_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C24h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C24h_EA_33_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_11_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_11_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_12_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_12_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_13_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_13_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_21_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_21_1_2"}
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{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_22_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_22_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_31_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_32_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_32_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_C48h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_Controls_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_C48h_EA_33_1_2"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"MDA-MB-231 parental and resistant (MDA-MB-231/R) cells were seeded at a density of 3 × 10^4 cells/cm2 onto 13.55 cm diameter Petri dishes, cultured in a humidified atmosphere of 5% CO2 at 37 ◦C and allowed to adhere for 24 h. After this, cells were incubated and collected at 0, 24 and 48 h, with basis on the population (25.5 ± 0.9 h and 30.6 ± 1.1 h for MDA-MB-231 and MDA-MB-231/R cells, respectively). At each time-point, cells were harvested using a 0.25% (v/v) trypsin-EDTA solution, washed twice with PBS and centrifuged (300 g, 5 min, 20 ◦C). The cell pellet was directly stored at − 80 ◦C until analysis. Three independent experiments with triplicates were performed for each cell type and time-point.","SAMPLE_TYPE":"Breast cancer cells","COLLECTION_DURATION":"Between 2 and 5 minutes","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"In this study, both cell types (MDA-MB-231 and MDA-MB-231/R) correspond to controls, so no treatment was applied to these two groups."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The cellular polar extracts were extracted using a biphasic extraction method of methanol/chloroform/water. Basically, cell pellets were resuspended in 650 µL of 80% (v/v) methanol-miliQ water solution, transferred to microcentrifuge tubes with 150 mg of glass beads, and vortexed for 5 min. Subsequently, 260 µL of 100% chloroform and 260 µL of 100% chloroform plus 220 µL MiliQ water were added to samples, which were vortexed for 5 min between solvents addition. The samples were kept at − 20 °C for 10 min and centrifuged. The aqueous phase of the resulting extract was collected into a new tube, vacuum-dried and stored at − 80 °C until the NMR analysis. Previously to NMR spectra acquision, the dry aqueous extracts were suspended in 650 µL of 100 mM sodium phosphate buffer (pH 7.4, in D2O containing 0.25% 3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid (TSP) for chemical shift referencing) and transferred into 5 mm NMR tubes","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"Biphasic method (methanol/ chloroform/ water)","EXTRACT_STORAGE":"-80℃"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","LABORATORY_NAME":"Metabolomics Ana M. Gil","SOFTWARE_VERSION":"Topspin 3.2","ACQUISITION_DATE":"February 2023"},

"NM":{"INSTRUMENT_NAME":"Avance III TM HD 500MHz","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","NMR_COMMENTS":"On folder 1 and folder pdata: 1st subfolder contains raw spectra; 2nd subfolder contains manually processed spectra","FIELD_FREQUENCY_LOCK":"Deuterium","SPECTROMETER_FREQUENCY":"500MHz","NMR_PROBE":"TXI","NMR_SOLVENT":"D2O","NMR_TUBE_SIZE":"5mm","SHIMMING_METHOD":"Topshim","RECEIVER_GAIN":"203","TEMPERATURE":"298K","NUMBER_OF_SCANS":"512","ACQUISITION_TIME":"2.34s","RELAXATION_DELAY":"2s","SPECTRAL_WIDTH":"7002.801","ZERO_FILLING":"64k","BASELINE_CORRECTION_METHOD":"Manual","CHEMICAL_SHIFT_REF_STD":"TSP (3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid)","NMR_RESULTS_FILE":"ST002720_AN004410_Results.txt UNITS:ppm"}

}