Summary of Study ST002982

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001307. The data can be accessed directly via it's Project DOI: 10.21228/M8S124 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002982
Study TitleMetabolic characterization of the polar endometabolome of Triple-Negative Breast Cancer parental and cDDP-resistant cells (part 2)
Study TypeNMR-based metabolomics of polar endometabolome of cultured cells
Study SummaryPlatinum (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
DepartmentDepartment of Chemistry and CICECO-Aveiro Institute of Materials
Last NameCarneiro
First NameTatiana João
AddressCampus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal
Emailtatiana.joao@ua.pt
Phone+351 234 370 200
Submit Date2023-11-20
Num Groups14
Total Subjects126
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2024-05-22
Release Version1
Tatiana João Carneiro Tatiana João Carneiro
https://dx.doi.org/10.21228/M8S124
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001307
Project DOI:doi: 10.21228/M8S124
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 drug-exposed tissues, unveiling insight into drug mechanisms and new markers of drug efficacy/toxicity. The present 1H NMR metabolomics study aims to characterize the in vivo response of the impact of a Pd(II)-complex with polyamine spermine (Pd2Spm), compared to cDDP, on the metabolism of several organs from healthy mice.
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 research was developed within the scope of the CICECO—Aveiro Institute of Materials, with references UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Por-tuguese Foundation for Science and Technology (FCT/MEC) and when appropriate co-financed by European Regional Development Fund (FEDER) under the PT2020 Partnership Agreement. This work was also funded by the FCT through LAQV/REQUIMTE FCT UIDB/50006/2020 (C.D.), UIDB/00070/2020 (A.L.M.B.d.C and M.P.M.M.), POCI-01-0145-FEDER-0016786, and Cen-tro-01-0145-FEDER-029956 (co-financed by COMPETE 2020, Portugal 2020 and European Com-munity through FEDER). We also acknowledge 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). M.V. thanks the FCT and the PhD Program in Medicines and Pharmaceutical Innovation (i3DU) for his PhD grant PD/BD/135460/2017 and T.J.C. thanks FCT for her PhD grant SFRH/BD/145920/2019; both grants were funded by the European Social Fund of the European Union and national funds FCT/MCTES.

Subject:

Subject ID:SU003095
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

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment_group
SA323554R_A24h_EA_21_1_2Resistant_cDDP_treated_24h
SA323555R_A24h_EA_32_1_2Resistant_cDDP_treated_24h
SA323556R_A24h_EA_33_1_2Resistant_cDDP_treated_24h
SA323557R_A24h_EA_11_1_2Resistant_cDDP_treated_24h
SA323558R_A24h_EA_31_1_2Resistant_cDDP_treated_24h
SA323559R_A24h_EA_23_1_2Resistant_cDDP_treated_24h
SA323560R_A24h_EA_13_1_2Resistant_cDDP_treated_24h
SA323561R_A24h_EA_22_1_2Resistant_cDDP_treated_24h
SA323562R_A24h_EA_12_1_2Resistant_cDDP_treated_24h
SA323563R_A48h_EA_22_1_2Resistant_cDDP_treated_48h
SA323564R_A48h_EA_33_1_2Resistant_cDDP_treated_48h
SA323565R_A48h_EA_12_1_2Resistant_cDDP_treated_48h
SA323566R_A48h_EA_11_1_2Resistant_cDDP_treated_48h
SA323567R_A48h_EA_21_1_2Resistant_cDDP_treated_48h
SA323568R_A48h_EA_13_1_2Resistant_cDDP_treated_48h
SA323569R_A48h_EA_23_1_2Resistant_cDDP_treated_48h
SA323570R_A48h_EA_32_1_2Resistant_cDDP_treated_48h
SA323571R_A48h_EA_31_1_2Resistant_cDDP_treated_48h
SA323509R_C0h_EA_32_1_2Resistant_Controls_0h
SA323510R_C0h_EA_33_1_2Resistant_Controls_0h
SA323511R_C0h_EA_11_1_2Resistant_Controls_0h
SA323512R_C0h_EA_23_1_2Resistant_Controls_0h
SA323513R_C0h_EA_31_1_2Resistant_Controls_0h
SA323514R_C0h_EA_12_1_2Resistant_Controls_0h
SA323515R_C0h_EA_21_1_2Resistant_Controls_0h
SA323516R_C0h_EA_13_1_2Resistant_Controls_0h
SA323517R_C0h_EA_22_1_2Resistant_Controls_0h
SA323518R_C24h_EA_32_1_2Resistant_Controls_24h
SA323519R_C24h_EA_33_1_2Resistant_Controls_24h
SA323520R_C24h_EA_23_1_2Resistant_Controls_24h
SA323521R_C24h_EA_31_1_2Resistant_Controls_24h
SA323522R_C24h_EA_11_1_2Resistant_Controls_24h
SA323523R_C24h_EA_22_1_2Resistant_Controls_24h
SA323524R_C24h_EA_13_1_2Resistant_Controls_24h
SA323525R_C24h_EA_12_1_2Resistant_Controls_24h
SA323526R_C24h_EA_21_1_2Resistant_Controls_24h
SA323527R_C48h_EA_21_1_2Resistant_Controls_48h
SA323528R_C48h_EA_11_1_2Resistant_Controls_48h
SA323529R_C48h_EA_12_1_2Resistant_Controls_48h
SA323530R_C48h_EA_22_1_2Resistant_Controls_48h
SA323531R_C48h_EA_13_1_2Resistant_Controls_48h
SA323532R_C48h_EA_31_1_2Resistant_Controls_48h
SA323533R_C48h_EA_23b_1_2Resistant_Controls_48h
SA323534R_C48h_EA_33_1_2Resistant_Controls_48h
SA323535R_C48h_EA_32_1_2Resistant_Controls_48h
SA323536R_B24h_EA_32_1_2Resistant_Pd2Spm_treated_24h
SA323537R_B24h_EA_23_1_2Resistant_Pd2Spm_treated_24h
SA323538R_B24h_EA_33_1_2Resistant_Pd2Spm_treated_24h
SA323539R_B24h_EA_31_1_2Resistant_Pd2Spm_treated_24h
SA323540R_B24h_EA_11_1_2Resistant_Pd2Spm_treated_24h
SA323541R_B24h_EA_22_1_2Resistant_Pd2Spm_treated_24h
SA323542R_B24h_EA_13_1_2Resistant_Pd2Spm_treated_24h
SA323543R_B24h_EA_12_1_2Resistant_Pd2Spm_treated_24h
SA323544R_B24h_EA_21_1_2Resistant_Pd2Spm_treated_24h
SA323545R_B48h_EA_32_1_2Resistant_Pd2Spm_treated_48h
SA323546R_B48h_EA_12_1_2Resistant_Pd2Spm_treated_48h
SA323547R_B48h_EA_31_1_2Resistant_Pd2Spm_treated_48h
SA323548R_B48h_EA_23_1_2Resistant_Pd2Spm_treated_48h
SA323549R_B48h_EA_13_1_2Resistant_Pd2Spm_treated_48h
SA323550R_B48h_EA_11_1_2Resistant_Pd2Spm_treated_48h
SA323551R_B48h_EA_33_1_2Resistant_Pd2Spm_treated_48h
SA323552R_B48h_EA_21_1_2Resistant_Pd2Spm_treated_48h
SA323553R_B48h_EA_22_1_2Resistant_Pd2Spm_treated_48h
SA323617S_A24h_EA_13_1_2Sensitive_cDDP_treated_24h
SA323618S_A24h_EA_31_1_2Sensitive_cDDP_treated_24h
SA323619S_A24h_EA_32_1_2Sensitive_cDDP_treated_24h
SA323620S_A24h_EA_33_1_2Sensitive_cDDP_treated_24h
SA323621S_A24h_EA_23_1_2Sensitive_cDDP_treated_24h
SA323622S_A24h_EA_22_1_2Sensitive_cDDP_treated_24h
SA323623S_A24h_EA_12_1_2Sensitive_cDDP_treated_24h
SA323624S_A24h_EA_21_1_2Sensitive_cDDP_treated_24h
SA323625S_A24h_EA_11_1_2Sensitive_cDDP_treated_24h
SA323626S_A48h_EA_13_1_2Sensitive_cDDP_treated_48h
SA323627S_A48h_EA_21_1_2Sensitive_cDDP_treated_48h
SA323628S_A48h_EA_12_1_2Sensitive_cDDP_treated_48h
SA323629S_A48h_EA_11_1_2Sensitive_cDDP_treated_48h
SA323630S_A48h_EA_22_1_2Sensitive_cDDP_treated_48h
SA323631S_A48h_EA_23_1_2Sensitive_cDDP_treated_48h
SA323632S_A48h_EA_32_1_2Sensitive_cDDP_treated_48h
SA323633S_A48h_EA_31_1_2Sensitive_cDDP_treated_48h
SA323634S_A48h_EA_33_1_2Sensitive_cDDP_treated_48h
SA323572S_C0h_EA_31_1_2Sensitive_Controls_0h
SA323573S_C0h_EA_32_1_2Sensitive_Controls_0h
SA323574S_C0h_EA_23_1_2Sensitive_Controls_0h
SA323575S_C0h_EA_33_1_2Sensitive_Controls_0h
SA323576S_C0h_EA_11_1_2Sensitive_Controls_0h
SA323577S_C0h_EA_22_1_2Sensitive_Controls_0h
SA323578S_C0h_EA_13_1_2Sensitive_Controls_0h
SA323579S_C0h_EA_12_1_2Sensitive_Controls_0h
SA323580S_C0h_EA_21_1_2Sensitive_Controls_0h
SA323581S_C24h_EA_32_1_2Sensitive_Controls_24h
SA323582S_C24h_EA_33_1_2Sensitive_Controls_24h
SA323583S_C24h_EA_23_1_2Sensitive_Controls_24h
SA323584S_C24h_EA_11_1_2Sensitive_Controls_24h
SA323585S_C24h_EA_31_1_2Sensitive_Controls_24h
SA323586S_C24h_EA_12_1_2Sensitive_Controls_24h
SA323587S_C24h_EA_21_1_2Sensitive_Controls_24h
SA323588S_C24h_EA_13_1_2Sensitive_Controls_24h
SA323589S_C24h_EA_22_1_2Sensitive_Controls_24h
SA323590S_C48h_EA_13_1_2Sensitive_Controls_48h
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 126

Collection:

Collection ID:CO003088
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 ID:TR003104
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%

Sample Preparation:

Sampleprep ID:SP003101
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 sodium salt (TSP-D4) 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 sodium salt (TSP-D4) for chemical shift referencing)

Analysis:

Analysis ID:AN004901
Analysis Type:NMR
Acquisition Date:March 2023
Software Version:Topspin 3.6.5
Operator Name:Tatiana João Carneiro
Results File:ST002982_AN004901_Results.txt
Units:ppm

NMR:

NMR ID:NM000270
Analysis ID:AN004901
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
Receiver Gain:203
Chemical Shift Ref Cpd:TSP-D4
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-D4
NMR Results File:TNBC_cells_untreated_treated_EA_NMR.txt UNITS:ppm
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