#METABOLOMICS WORKBENCH VeronicaGhini_20220322_130847 DATATRACK_ID:3133 STUDY_ID:ST002116 ANALYSIS_ID:AN003464 PROJECT_ID:PR001341
VERSION             	1
CREATED_ON             	March 23, 2022, 2:34 am
#PROJECT
PR:PROJECT_TITLE                 	Comparative NMR metabolomics of the responses of A2780 human ovarian cancer
PR:PROJECT_TITLE                 	cells to clinically established Pt based drugs
PR:PROJECT_SUMMARY               	Pt based drugs play a very important role in current cancer treatment; yet their
PR:PROJECT_SUMMARY               	cellular and mechanistic aspects are not fully understood. NMR metabolomics
PR:PROJECT_SUMMARY               	provides a powerful tool to investigate the metabolic perturbations induced by
PR:PROJECT_SUMMARY               	Pt drugs in cancer cells and decipher their meaning in relation to the presumed
PR:PROJECT_SUMMARY               	molecular mechanisms. We have carried out a systematic and comparative NMR
PR:PROJECT_SUMMARY               	metabolomics study to analyze the responses of A2780 human ovarian cancer cells
PR:PROJECT_SUMMARY               	to the main clinically established Pt drugs, i.e. cisplatin, carboplatin and
PR:PROJECT_SUMMARY               	oxaliplatin, with a particular attention for the oxaliplatin/cisplatin
PR:PROJECT_SUMMARY               	comparison in view of recently described mechanistic differences. Notably, NMR
PR:PROJECT_SUMMARY               	analysis revealed some moderate and consistent changes in the metabolomic
PR:PROJECT_SUMMARY               	profiles of A2780 cells treated with the 3 Pt drugs with respect to controls but
PR:PROJECT_SUMMARY               	only very small differences among them. Beyond the expected alterations at the
PR:PROJECT_SUMMARY               	level of the nucleic acids the observed changes highlight in all cases induction
PR:PROJECT_SUMMARY               	of a significant ER stress. Owing to the clinical relevance of platinum
PR:PROJECT_SUMMARY               	resistance the behavior of a cisplatin resistant A2780 cancer cell line upon
PR:PROJECT_SUMMARY               	cisplatin treatment was also evaluated.
PR:INSTITUTE                     	University of Florence
PR:DEPARTMENT                    	Department of Chemistry
PR:LABORATORY                    	Metabolomics
PR:LAST_NAME                     	Ghini
PR:FIRST_NAME                    	Veronica
PR:ADDRESS                       	via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
PR:EMAIL                         	ghini@cerm.unifi.it
PR:PHONE                         	+39 3922800462
#STUDY
ST:STUDY_TITLE                   	Comparative NMR metabolomics of the responses of A2780 human ovarian cancer
ST:STUDY_TITLE                   	cells to clinically established Pt based drugs
ST:STUDY_SUMMARY                 	Pt based drugs play a very important role in current cancer treatment; yet their
ST:STUDY_SUMMARY                 	cellular and mechanistic aspects are not fully understood. NMR metabolomics
ST:STUDY_SUMMARY                 	provides a powerful tool to investigate the metabolic perturbations induced by
ST:STUDY_SUMMARY                 	Pt drugs in cancer cells and decipher their meaning in relation to the presumed
ST:STUDY_SUMMARY                 	molecular mechanisms. We have carried out a systematic and comparative NMR
ST:STUDY_SUMMARY                 	metabolomics study to analyze the responses of A2780 human ovarian cancer cells
ST:STUDY_SUMMARY                 	to the main clinically established Pt drugs, i.e. cisplatin, carboplatin and
ST:STUDY_SUMMARY                 	oxaliplatin, with a particular attention for the oxaliplatin/cisplatin
ST:STUDY_SUMMARY                 	comparison in view of recently described mechanistic differences. Notably, NMR
ST:STUDY_SUMMARY                 	analysis revealed some moderate and consistent changes in the metabolomic
ST:STUDY_SUMMARY                 	profiles of A2780 cells treated with the 3 Pt drugs with respect to controls but
ST:STUDY_SUMMARY                 	only very small differences among them. Beyond the expected alterations at the
ST:STUDY_SUMMARY                 	level of the nucleic acids the observed changes highlight in all cases induction
ST:STUDY_SUMMARY                 	of a significant ER stress. Owing to the clinical relevance of platinum
ST:STUDY_SUMMARY                 	resistance the behavior of a cisplatin resistant A2780 cancer cell line upon
ST:STUDY_SUMMARY                 	cisplatin treatment was also evaluated.
ST:INSTITUTE                     	University of Florence
ST:DEPARTMENT                    	Department of Chemistry
ST:LABORATORY                    	Metabolomics
ST:LAST_NAME                     	Ghini
ST:FIRST_NAME                    	Veronica
ST:ADDRESS                       	via Luigi Sacconi 6
ST:EMAIL                         	turano@cerm.unifi.it
ST:PHONE                         	+390554574266
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:CELL_STRAIN_DETAILS           	A2780 ovarian cancer cells
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	Cell-Carbo-24h-1	sample_type:lysate | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Carbo-24h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Carbo-24h-2	sample_type:lysate | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Carbo-24h-2
SUBJECT_SAMPLE_FACTORS           	-	Cell-CARBO-24h-4	sample_type:lysate | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-CARBO-24h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Carbo-48h-1	sample_type:lysate | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Carbo-48h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Carbo-48h-3	sample_type:lysate | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Carbo-48h-3
SUBJECT_SAMPLE_FACTORS           	-	Cell-Carbo-48h-4	sample_type:lysate | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Carbo-48h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-24h-1	sample_type:lysate | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Cis-24h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-24h-2	sample_type:lysate | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Cis-24h-2
SUBJECT_SAMPLE_FACTORS           	-	Cell-CIS-24h-4	sample_type:lysate | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-CIS-24h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-48h-1	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Cis-48h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-48h-3	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Cis-48h-3
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-48h-4	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Cis-48h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-24h-1	sample_type:lysate | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-24h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-24h-2	sample_type:lysate | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-24h-2
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-24h-4	sample_type:lysate | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-24h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-48h-1	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-48h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-48h-3	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-48h-3
SUBJECT_SAMPLE_FACTORS           	-	Cell-Ctr-48h-4	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Ctr-48h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Oxa-24h-1	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Oxa-24h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Oxa-24h-2	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-Oxa-24h-2
SUBJECT_SAMPLE_FACTORS           	-	Cell-OXA-24h-4	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=Cell-OXA-24h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Oxa-48h-1	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Oxa-48h-1
SUBJECT_SAMPLE_FACTORS           	-	Cell-Oxa-48h-3	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Oxa-48h-3
SUBJECT_SAMPLE_FACTORS           	-	Cell-Oxa-48h-4	sample_type:lysate | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=Cell-Oxa-48h-4
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-R-48h-1-1411	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cis-R-48h-1-1411
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-R-48h-2-2110	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cis-R-48h-2-2110
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cis-R-48h-3-2810	sample_type:lysate | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cis-R-48h-3-2810
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cont-R-48h-1-1411	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cont-R-48h-1-1411
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cont-R-48h-2-2110	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cont-R-48h-2-2110
SUBJECT_SAMPLE_FACTORS           	-	Cell-Cont-R-48h-3-2810	sample_type:lysate | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=Cell-Cont-R-48h-3-2810
SUBJECT_SAMPLE_FACTORS           	-	SN-CARBO-24h-1	sample_type:medium | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CARBO-24h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CARBO-24h-2	sample_type:medium | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CARBO-24h-2
SUBJECT_SAMPLE_FACTORS           	-	SN-Carbo-24h-4	sample_type:medium | treatment_type:carboplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-Carbo-24h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CARBO-48h-1	sample_type:medium | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CARBO-48h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CARBO-48h-3	sample_type:medium | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CARBO-48h-3
SUBJECT_SAMPLE_FACTORS           	-	SN-CARBO-48h-4	sample_type:medium | treatment_type:carboplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CARBO-48h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-24h-1	sample_type:medium | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CIS-24h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-24h-2	sample_type:medium | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CIS-24h-2
SUBJECT_SAMPLE_FACTORS           	-	SN-Cis-24h-4	sample_type:medium | treatment_type:cisplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-Cis-24h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-48h-1	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CIS-48h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-48h-3	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CIS-48h-3
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-48h-4	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CIS-48h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CTR-24h-1	sample_type:medium | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CTR-24h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CTR-24h-2	sample_type:medium | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-CTR-24h-2
SUBJECT_SAMPLE_FACTORS           	-	SN-Ctr-24h-4	sample_type:medium | treatment_type:control | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-Ctr-24h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CTR-48h-1	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CTR-48h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-CTR-48h-3	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CTR-48h-3
SUBJECT_SAMPLE_FACTORS           	-	SN-CTR-48h-4	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-CTR-48h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-OXA-24h-1	sample_type:medium | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-OXA-24h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-OXA-24h-2	sample_type:medium | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-OXA-24h-2
SUBJECT_SAMPLE_FACTORS           	-	SN-Oxa-24h-4	sample_type:medium | treatment_type:oxaliplatin | treatment_time:24 | cell_line:A2780	RAW_FILE_NAME=SN-Oxa-24h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-OXA-48h-1	sample_type:medium | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-OXA-48h-1
SUBJECT_SAMPLE_FACTORS           	-	SN-OXA-48h-3	sample_type:medium | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-OXA-48h-3
SUBJECT_SAMPLE_FACTORS           	-	SN-OXA-48h-4	sample_type:medium | treatment_type:oxaliplatin | treatment_time:48 | cell_line:A2780	RAW_FILE_NAME=SN-OXA-48h-4
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-R-48h-1-1411	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-CIS-R-48h-1-1411
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-R-48h-2-2110	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-CIS-R-48h-2-2110
SUBJECT_SAMPLE_FACTORS           	-	SN-CIS-R-48h-3-2810	sample_type:medium | treatment_type:cisplatin | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-CIS-R-48h-3-2810
SUBJECT_SAMPLE_FACTORS           	-	SN-Cont-R-48h-1-1411	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-Cont-R-48h-1-1411
SUBJECT_SAMPLE_FACTORS           	-	SN-Cont-R-48h-2-2110	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-Cont-R-48h-2-2110
SUBJECT_SAMPLE_FACTORS           	-	SN-Cont-R-48h-3-2810	sample_type:medium | treatment_type:control | treatment_time:48 | cell_line:A2780cp	RAW_FILE_NAME=SN-Cont-R-48h-3-2810
#COLLECTION
CO:COLLECTION_SUMMARY            	A2780 cells were purchase from Sigma-Aldrich and derived from the European
CO:COLLECTION_SUMMARY            	Collection of Authenticated Cell Culture (human ovarian carcinoma; catalogue
CO:COLLECTION_SUMMARY            	no.: 93112519; lot no.13J012, passage no.: P + 9). A2780cp cells were kindly
CO:COLLECTION_SUMMARY            	provided by Dr Simona Bracini and were obtained via prolonged exposition to
CO:COLLECTION_SUMMARY            	sub-lethal dose of cisplatin. Cells were maintained in RPMI1640 medium
CO:COLLECTION_SUMMARY            	supplemented with 2 mM glutamine, 10% of FCS and antibiotics at 37 °C in a 5%
CO:COLLECTION_SUMMARY            	CO2 atmosphere and sub-cultured twice weekly. Split 1:5 (3–6 × 10^4 cells per
CO:COLLECTION_SUMMARY            	mL).
CO:SAMPLE_TYPE                   	Cultured cells
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	For drug treatment, 2.7 *10^6 A2780 cells were seeded in p100 plate and after 24
TR:TREATMENT_SUMMARY             	hours were exposed to a concentration of the three Pt-drugs, i.e. CIS, OXA and
TR:TREATMENT_SUMMARY             	CARBO equal to their 72 h-exposure IC50 value (2.5, 55 and 0.46 uM,
TR:TREATMENT_SUMMARY             	respectively). The drug incubations were stopped at two different time points,
TR:TREATMENT_SUMMARY             	24 h and 48 h. The A2780cp cells were exposed to a concentration of cisplatin
TR:TREATMENT_SUMMARY             	equal to their 72 h-exposure IC50 value (15 uM). The drug incubation was stopped
TR:TREATMENT_SUMMARY             	after 48 h of treatment.
TR:TREATMENT                     	Cisplatin, carboplatin and oxaliplatin
TR:CELL_MEDIA                    	RPMI1640
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Frozen samples were thawed at room temperature and shaken before use. For cell
SP:SAMPLEPREP_SUMMARY            	lysates, 50 μl of 2H2O were added to 450 μl of each lysate sample. In the case
SP:SAMPLEPREP_SUMMARY            	of cell culture media, 300 μl of sodium phosphate buffer (70 mM Na2HPO4; 20%
SP:SAMPLEPREP_SUMMARY            	v/v 2H2O; 4.6 mM TMSP, pH 7.4) was added to 300 μl of each medium sample. The
SP:SAMPLEPREP_SUMMARY            	mixtures were homogenized by vortexing for 30 s and transferred into 5 mm NMR
SP:SAMPLEPREP_SUMMARY            	tubes (Bruker BioSpin srl) for analysis.
#ANALYSIS
AN:ANALYSIS_TYPE                 	NMR
AN:LABORATORY_NAME               	Metabolomics
#NMR
NM:INSTRUMENT_NAME               	Bruker Advance 600 MHZ
NM:INSTRUMENT_TYPE               	FT-NMR
NM:NMR_EXPERIMENT_TYPE           	1D-1H
NM:SPECTROMETER_FREQUENCY        	600 MHz
NM:NMR_TUBE_SIZE                 	5,00 mm
NM:WATER_SUPPRESSION             	water presaturation
NM:TEMPERATURE                   	300 K for lysates and 31o for media
NM:NMR_RESULTS_FILE               	ST002116_AN003464_Results.txt	UNITS:ppm
#END