{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002982","ANALYSIS_ID":"AN004901","VERSION":"1","CREATED_ON":"November 20, 2023, 3:56 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 polar endometabolome of both MDA-MB-231 cDDP-sensitve and cDDP-resistant cell lines, 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","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana João","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351 234 370 200","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, UIDB/00070/2020 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). We also acknowledge FCT for Ph.D. grants SFRH/BD/145920/2019 and PD/BD/135460/2017, both grants 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 (part 2)","STUDY_TYPE":"NMR-based metabolomics of polar endometabolome of cultured cells","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 effects of cDDP and Pd2Spm on the polar endometabolome of both MDA-MB-231 cDDP-sensitive and cDDP-resistant cell lines, aiming to describe metabolic markers of (i) resistance upon cDDP treatment, and (ii) the effect of Pd2Spm on the established cDDP-resistant cells. The former observations will give helpful insights about the metabolic features of cDDP-resistance during treatment, and enlighten on the potential role of Pd2Spm in metabolically affecting/tackling cDDP-resistance.","INSTITUTE":"University of Aveiro","DEPARTMENT":"Department of Chemistry and CICECO-Aveiro Institute of Materials","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana João","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351 234 370 200","NUM_GROUPS":"14","TOTAL_SUBJECTS":"126"},

"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":"Inferior to 10","CELL_COUNTS":"5 M"},
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"Sample ID":"S_A24h_EA_22_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A24h_EA_22_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A24h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A24h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A24h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A24h_EA_31_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A24h_EA_32_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A24h_EA_32_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A24h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A24h_EA_33_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_11_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_11_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_12_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_12_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_13_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_13_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_21_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_21_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_22_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_22_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_31_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_32_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_32_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B24h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_24h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B24h_EA_33_1_2"}
},
{
"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"}
},
{
"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"}
},
{
"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"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_11_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_11_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_12_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_12_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_13_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_13_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_21_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_21_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_22_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_22_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_31_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_32_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_32_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_A48h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_cDDP_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_A48h_EA_33_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_11_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_11_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_12_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_12_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_13_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_13_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_21_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_21_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_22_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_22_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_23_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_23_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_31_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_31_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_32_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_32_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"S_B48h_EA_33_1_2",
"Factors":{"Treatment_group":"Sensitive_Pd2Spm_treated_48h"},
"Additional sample data":{"RAW_FILE_NAME":"S_B48h_EA_33_1_2"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"MDA-MB-231 parental and MDA-MB-231/R cDDP-resistant cell lines 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 (t = 0 h). After this, the experiment was initiated by adding stock solutions of each drug to achieve the corresponding half of maximal inhibitory effect IC50 values: 1.0 µM cDDP and 7.9 μM Pd2Spm. Phosphate-buffer saline was used in control groups. Then, cells were incubated and collected at t = 24 h and t = 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":"Epithelial cells","COLLECTION_METHOD":"Trypsinization for cells harvesting followed by pellet collection and storage at − 80 ◦C (until extract prepatation)","COLLECTION_FREQUENCY":"One collection per sample replicate","COLLECTION_DURATION":"Between 2 and 5 minutes","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were treated during culture time by adding drugs stock solution to the growth culture medium. Briefly, after seeding, cells were allowed to adhere for 24 h (t = 0 h). After this, the experiment was initiated by adding stock solutions of each drug to achieve the corresponding half of maximal inhibitory effect IC50 values: 1.0 µM cDDP and 7.9 μM Pd2Spm. Phosphate-buffered saline (PBS) was used in control groups. Then, cells were incubated and collected at t = 24 h and t = 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).","TREATMENT_COMPOUND":"cDDP or Pd2Spm (PBS for controls)","TREATMENT_ROUTE":"Dissolution of drugs stock solutions into the culture medium","TREATMENT_DOSE":"1.0 µM cDDP and 7.9 μM Pd2Spm","TREATMENT_DOSEVOLUME":"5.5 mL","TREATMENT_DOSEDURATION":"24 h and 48 h","TREATMENT_VEHICLE":"Phosphate-buffered saline (PBS)","CELL_MEDIA":"Dulbecco’s Modified Eagle’s Medium—high-glucose cell growth medium (DMEM-HG)","CELL_ENVIR_COND":"Humidified atmosphere of 5% CO2 at 37 ◦C","CELL_HARVESTING":"Tripsinization","CELL_PCT_CONFLUENCE":"~ 70 to 80%"},

"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. All samples and reagents were kept in ice during the extraction procedure. Before NMR analysis, 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":"On ice","EXTRACTION_METHOD":"Biphasic extraction method of methanol/chloroform/water","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"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)"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","OPERATOR_NAME":"Tatiana João Carneiro","SOFTWARE_VERSION":"Topspin 3.6.5","ACQUISITION_DATE":"March 2023"},

"NM":{"INSTRUMENT_NAME":"Avance III HD","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","NMR_COMMENTS":"1st subfolder contains raw spectra; 2nd subfolder contains manually processed spectra","FIELD_FREQUENCY_LOCK":"D2O","SPECTROMETER_FREQUENCY":"500 MHz","NMR_PROBE":"5 mm TXI probe","NMR_SOLVENT":"100% D2O","NMR_TUBE_SIZE":"5mm","SHIMMING_METHOD":"Automatic and manual","PULSE_SEQUENCE":"Noesypr1d from Bruker library","RECEIVER_GAIN":"203","CHEMICAL_SHIFT_REF_CPD":"TSP","TEMPERATURE":"298K","NUMBER_OF_SCANS":"512","DUMMY_SCANS":"4 s","ACQUISITION_TIME":"2.34 s","RELAXATION_DELAY":"2 s","SPECTRAL_WIDTH":"7002.801 Hz","NUM_DATA_POINTS_ACQUIRED":"32 k","REAL_DATA_POINTS":"64 k","LINE_BROADENING":"0.3 Hz (multiplication)","BASELINE_CORRECTION_METHOD":"Manual","CHEMICAL_SHIFT_REF_STD":"TSP","NMR_RESULTS_FILE":"ST002982_AN004901_Results.txt UNITS:ppm"}

}